From e15eb3b27f2896a636bc7c7da07b3b1b9ba67fcb Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 12:46:50 -0700
Subject: [PATCH 001/173] Templates: Add upload status indicators to index

---
 app/templates/index.html | 51 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 46 insertions(+), 5 deletions(-)

diff --git a/app/templates/index.html b/app/templates/index.html
index b9976bf..0444aa1 100644
--- a/app/templates/index.html
+++ b/app/templates/index.html
@@ -88,9 +88,30 @@ <h1 class="text-2xl font-bold text-gray-900">Upload MCAP Files</h1>
         <div class="px-6 py-2 bg-blue-50 border-b border-gray-200 flex items-center justify-between">
             <span class="text-sm text-blue-800" title="Does not include files in subfolders">
                 <span id="folder-mcap-count">0</span> MCAP files in this folder (not subfolders)
+                <span id="browser-root-upload-status" class="ml-2"></span>
             </span>
         </div>
 
+        <!-- Browser Scan Status Bar -->
+        <div id="browser-scan-status" class="hidden px-6 py-2 bg-green-50 border-b border-gray-200">
+            <div class="flex items-center justify-between">
+                <div class="flex items-center space-x-2">
+                    <svg id="browser-scan-spinner" class="animate-spin h-4 w-4 text-nlr-blue" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
+                        <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
+                        <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
+                    </svg>
+                    <span id="browser-scan-text" class="text-sm text-gray-700">
+                        Scanning folders...
+                    </span>
+                </div>
+                <label class="flex items-center">
+                    <input type="checkbox" id="browser-hide-uploaded"
+                           class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
+                    <span class="ml-2 text-sm text-gray-600">Hide uploaded folders</span>
+                </label>
+            </div>
+        </div>
+
         <!-- Folder List (subfolders) -->
         <div id="folder-list" class="divide-y divide-gray-200">
             <!-- Folders will be inserted here -->
@@ -161,6 +182,19 @@ <h2 class="text-lg font-semibold text-gray-900">Review Selected Files</h2>
                     {{ stat_card("scan-already-uploaded", "Already Uploaded", "yellow") }}
                 </div>
 
+                <!-- Scan Progress Indicator -->
+                <div id="scan-progress-container" class="hidden mb-4">
+                    <div class="flex items-center space-x-3 px-4 py-3 bg-blue-50 rounded-lg">
+                        <svg class="animate-spin h-5 w-5 text-nlr-blue" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
+                            <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
+                            <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
+                        </svg>
+                        <span id="scan-progress-text" class="text-sm text-blue-800">
+                            Scanning folders...
+                        </span>
+                    </div>
+                </div>
+
                 <div class="flex justify-center space-x-4">
                     <button id="cancel-scan-btn"
                             class="px-6 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 transition-colors flex items-center">
@@ -182,11 +216,18 @@ <h2 class="text-lg font-semibold text-gray-900">Review Selected Files</h2>
             <!-- Sortable File Table -->
             <div class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center justify-between">
                 <span class="text-sm font-medium text-gray-700">Files</span>
-                <label class="flex items-center">
-                    <input type="checkbox" id="scan-hide-uploaded"
-                           class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
-                    <span class="ml-2 text-sm text-gray-600">Hide already uploaded</span>
-                </label>
+                <div class="flex items-center space-x-4">
+                    <label class="flex items-center">
+                        <input type="checkbox" id="scan-hide-completed-folders"
+                               class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
+                        <span class="ml-2 text-sm text-gray-600">Hide completed folders</span>
+                    </label>
+                    <label class="flex items-center">
+                        <input type="checkbox" id="scan-hide-uploaded"
+                               class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
+                        <span class="ml-2 text-sm text-gray-600">Hide already uploaded</span>
+                    </label>
+                </div>
             </div>
             <div class="overflow-x-auto">
                 <table class="w-full divide-y divide-gray-200 table-fixed">

From 95bfb5c4a036eb1590db454d097322a7047ea52c Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 12:47:35 -0700
Subject: [PATCH 002/173] Service: Use SSE to list files for upload vs cache

---
 app/routes/upload.py           | 108 +++++++++++-
 app/services/upload_manager.py | 306 ++++++++++++++++++++++++++++++---
 2 files changed, 387 insertions(+), 27 deletions(-)

diff --git a/app/routes/upload.py b/app/routes/upload.py
index 0010c50..326606a 100644
--- a/app/routes/upload.py
+++ b/app/routes/upload.py
@@ -204,8 +204,11 @@ def generate() -> Generator[str, None, None]:
         try:
             # Send initial state
             job = manager.get_job(job_id)
+            scan_job = manager.get_scan_job(job_id) if not job else None
             if job:
                 yield f"data: {json.dumps(job.to_dict())}\n\n"
+            elif scan_job:
+                yield f"data: {json.dumps({'type': 'scan_initial', 'status': scan_job.status})}\n\n"
 
             # Stream updates
             while True:
@@ -214,19 +217,60 @@ def generate() -> Generator[str, None, None]:
                     data = queue.popleft()
                     yield f"data: {json.dumps(data)}\n\n"
 
-                    # Check if job is complete
+                    # Check if job is complete (upload jobs)
                     if data.get("status") in ("completed", "failed", "cancelled"):
-                        return
+                        # For scan events, check the type field
+                        if data.get("type") == "scan_complete":
+                            return
+                        # For upload jobs (no type field)
+                        if not data.get("type"):
+                            return
 
                 # Small delay to prevent busy waiting
                 time.sleep(0.1)
 
-                # Check if job still exists
+                # Check if job still exists (upload or scan)
                 job = manager.get_job(job_id)
-                if not job:
+                scan_job = manager.get_scan_job(job_id) if not job else None
+                if not job and not scan_job:
                     yield 'data: {"error": "Job not found"}\n\n'
                     return
 
+                # Check if scan job reached terminal state before client connected
+                # (race condition: fast scans finish before EventSource opens,
+                # so events were sent to empty queues and dropped)
+                if scan_job and scan_job.status in (
+                    "completed",
+                    "failed",
+                    "cancelled",
+                ):
+                    # Replay missed folder results so frontend gets the data
+                    for folder_data in scan_job.scanned_folders:
+                        replay_event = {
+                            "type": "scan_folder_complete",
+                            "folder": folder_data,
+                            "folders_scanned": scan_job.folders_scanned,
+                            "folders_total": scan_job.folders_total,
+                            "running_totals": {
+                                "total_files_found": scan_job.total_files_found,
+                                "total_already_uploaded": scan_job.total_already_uploaded,
+                                "total_size": scan_job.total_size,
+                            },
+                        }
+                        yield f"data: {json.dumps(replay_event)}\n\n"
+
+                    terminal_data = {
+                        "type": "scan_complete",
+                        "status": scan_job.status,
+                        "folders_scanned": scan_job.folders_scanned,
+                        "folders_total": scan_job.folders_total,
+                        "total_files_found": scan_job.total_files_found,
+                        "total_already_uploaded": scan_job.total_already_uploaded,
+                        "total_size": scan_job.total_size,
+                    }
+                    yield f"data: {json.dumps(terminal_data)}\n\n"
+                    return
+
         finally:
             # Clean up queue
             with _sse_lock:
@@ -313,6 +357,8 @@ def cancel_upload(job_id: str) -> tuple[Response, int]:
                 "job": job.to_dict() if job else None,
             }
         ), 200
+    elif manager.cancel_scan_job(job_id):
+        return jsonify({"success": True, "job_id": job_id}), 200
     else:
         return jsonify({"error": "Job not found"}), 404
 
@@ -374,6 +420,60 @@ def scan_folder() -> tuple[Response, int]:
     ), 200
 
 
+@upload_bp.route("/scan-folder-async", methods=["POST"])
+def scan_folder_async() -> tuple[Response, int]:
+    """Start an async folder scan that streams results via SSE.
+
+    Request body:
+        folder_path: Path to the folder to scan
+
+    Returns:
+        JSON response with job_id (202 Accepted)
+    """
+    if not request.is_json:
+        return jsonify({"error": "JSON body required"}), 400
+
+    data = request.get_json()
+    if not data or "folder_path" not in data:
+        return jsonify({"error": "folder_path is required"}), 400
+
+    folder_path = Path(data["folder_path"])
+
+    if not folder_path.exists():
+        return jsonify({"error": f"Folder not found: {folder_path}"}), 404
+
+    if not folder_path.is_dir():
+        return jsonify({"error": f"Path is not a directory: {folder_path}"}), 400
+
+    cache_only: bool = data.get("cache_only", False)
+
+    settings = get_settings()
+    manager = get_upload_manager()
+
+    scan_job = manager.create_scan_job(str(folder_path.absolute()))
+
+    def scan_progress_callback(job_id: str, event_data: dict[str, Any]) -> None:
+        send_sse_event(job_id, event_data)
+
+    def run_scan() -> None:
+        manager.scan_folder_async(
+            scan_job.job_id,
+            settings.s3_bucket,
+            settings.aws_profile,
+            settings.aws_region,
+            progress_callback=scan_progress_callback,
+            cache_only=cache_only,
+        )
+
+    thread = threading.Thread(target=run_scan, daemon=True)
+    thread.start()
+
+    return jsonify({
+        "job_id": scan_job.job_id,
+        "status": "scanning",
+    }), 202
+
+
 @upload_bp.route("/bulk-analyze", methods=["POST"])
 def bulk_analyze() -> tuple[Response, int]:
     """Bulk analyze files with pre-filtering and optional auto-upload.
diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index 15aa369..dffcb1f 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -240,11 +240,43 @@ def to_dict(self) -> dict[str, Any]:
         }
 
 
+@dataclass
+class ScannedFolder:
+    """Results for a single scanned subfolder."""
+
+    folder_path: str
+    relative_path: str
+    files: list[dict[str, Any]]
+    total_files: int = 0
+    already_uploaded: int = 0
+    all_uploaded: bool = False
+    error: str | None = None
+
+
+@dataclass
+class ScanJob:
+    """Tracks an async folder scan job."""
+
+    job_id: str
+    root_folder: str
+    status: str = "scanning"  # scanning | completed | failed | cancelled
+    cancelled: bool = False
+    folders_scanned: int = 0
+    folders_total: int = 0
+    total_files_found: int = 0
+    total_already_uploaded: int = 0
+    total_size: int = 0
+    scanned_folders: list[dict[str, Any]] = field(default_factory=list)
+    created_at: datetime = field(default_factory=lambda: datetime.now(UTC))
+    lock: threading.Lock = field(default_factory=threading.Lock, repr=False)
+
+
 class UploadManager:
     """Manages upload jobs and their execution."""
 
     def __init__(self, max_workers: int = 4) -> None:
         self.jobs: dict[str, UploadJob] = {}
+        self.scan_jobs: dict[str, ScanJob] = {}
         self.max_workers = max_workers
         self._lock = threading.Lock()
 
@@ -969,6 +1001,7 @@ def pre_filter_files(
         s3_bucket: str,
         aws_profile: str = "default",
         aws_region: str = "us-west-2",
+        cache_only: bool = False,
     ) -> tuple[list[str], dict[str, Any]]:
         """Pre-filter files using cache and filename timestamp extraction.
 
@@ -1062,37 +1095,264 @@ def pre_filter_files(
 
         # Batch S3 HEAD checks for cache misses
         if cache_miss_s3_paths:
-            try:
-                s3_client = s3_service.create_s3_client(aws_profile, aws_region)
+            if cache_only:
+                # In cache_only mode, skip S3 HEAD checks — treat misses as not-uploaded
+                for idx in cache_miss_indices:
+                    files_to_analyze.append(file_statuses[idx]["path"])
+            else:
+                try:
+                    s3_client = s3_service.create_s3_client(aws_profile, aws_region)
 
-                def check_s3(s3_path: str) -> bool:
-                    return s3_service.check_file_exists(s3_client, s3_bucket, s3_path)
+                    def check_s3(s3_path: str) -> bool:
+                        return s3_service.check_file_exists(s3_client, s3_bucket, s3_path)
 
-                with ThreadPoolExecutor(max_workers=self.max_workers) as executor:
-                    results = list(executor.map(check_s3, cache_miss_s3_paths))
+                    with ThreadPoolExecutor(max_workers=self.max_workers) as executor:
+                        results = list(executor.map(check_s3, cache_miss_s3_paths))
 
-                for idx, s3_path, exists in zip(
-                    cache_miss_indices, cache_miss_s3_paths, results, strict=True
-                ):
-                    # Update cache with result
-                    fs = file_statuses[idx]
-                    cache.update_cache(
-                        s3_bucket, s3_path, exists, fs["filename"], fs["size"]
-                    )
-                    if exists:
-                        stats["s3_hits"] += 1
-                        fs["already_uploaded"] = True
-                    else:
-                        files_to_analyze.append(fs["path"])
-            except Exception:
-                # S3 check failed — fall back to full analysis for cache misses
-                for idx in cache_miss_indices:
-                    files_to_analyze.append(file_statuses[idx]["path"])
+                    for idx, s3_path, exists in zip(
+                        cache_miss_indices, cache_miss_s3_paths, results, strict=True
+                    ):
+                        # Update cache with result
+                        fs = file_statuses[idx]
+                        cache.update_cache(
+                            s3_bucket, s3_path, exists, fs["filename"], fs["size"]
+                        )
+                        if exists:
+                            stats["s3_hits"] += 1
+                            fs["already_uploaded"] = True
+                        else:
+                            files_to_analyze.append(fs["path"])
+                except Exception:
+                    # S3 check failed — fall back to full analysis for cache misses
+                    for idx in cache_miss_indices:
+                        files_to_analyze.append(file_statuses[idx]["path"])
 
         stats["to_analyze"] = len(files_to_analyze)
         stats["file_statuses"] = file_statuses
         return files_to_analyze, stats
 
+    def create_scan_job(self, folder_path: str) -> ScanJob:
+        """Create a new scan job for a folder.
+
+        Args:
+            folder_path: Root folder to scan
+
+        Returns:
+            The created ScanJob
+        """
+        job_id = str(uuid.uuid4())
+        scan_job = ScanJob(job_id=job_id, root_folder=folder_path)
+        with self._lock:
+            self.scan_jobs[job_id] = scan_job
+        return scan_job
+
+    def get_scan_job(self, job_id: str) -> ScanJob | None:
+        """Get a scan job by ID."""
+        return self.scan_jobs.get(job_id)
+
+    def cancel_scan_job(self, job_id: str) -> bool:
+        """Cancel a scan job.
+
+        Args:
+            job_id: The scan job ID to cancel
+
+        Returns:
+            True if job was found and cancelled
+        """
+        scan_job = self.get_scan_job(job_id)
+        if not scan_job:
+            return False
+        scan_job.cancelled = True
+        scan_job.status = "cancelled"
+        return True
+
+    def scan_folder_async(
+        self,
+        job_id: str,
+        s3_bucket: str,
+        aws_profile: str,
+        aws_region: str,
+        progress_callback: Callable[[str, dict[str, Any]], None] | None = None,
+        cache_only: bool = False,
+    ) -> None:
+        """Scan a folder asynchronously, processing subfolder by subfolder.
+
+        Args:
+            job_id: The scan job ID
+            s3_bucket: S3 bucket for duplicate checking
+            aws_profile: AWS profile for S3 access
+            aws_region: AWS region for S3 access
+            progress_callback: Called with (job_id, event_data) for each event
+        """
+        scan_job = self.get_scan_job(job_id)
+        if not scan_job:
+            return
+
+        root = Path(scan_job.root_folder)
+        log = get_log_service()
+
+        try:
+            # Phase 1: Enumerate subfolders containing .mcap files (fast, metadata only)
+            folder_map: dict[str, list[Path]] = {}
+            for mcap_path in root.rglob("*.mcap"):
+                if scan_job.cancelled:
+                    break
+                if mcap_path.is_file():
+                    parent = str(mcap_path.parent)
+                    if parent not in folder_map:
+                        folder_map[parent] = []
+                    folder_map[parent].append(mcap_path)
+
+            if scan_job.cancelled:
+                if progress_callback:
+                    progress_callback(job_id, {
+                        "type": "scan_complete",
+                        "status": "cancelled",
+                    })
+                return
+
+            scan_job.folders_total = len(folder_map)
+
+            if progress_callback:
+                progress_callback(job_id, {
+                    "type": "scan_started",
+                    "folders_total": scan_job.folders_total,
+                    "root_folder": scan_job.root_folder,
+                })
+
+            # Phase 2: Process each subfolder
+            for folder_path_str, mcap_paths in sorted(folder_map.items()):
+                if scan_job.cancelled:
+                    break
+
+                try:
+                    relative_path = str(Path(folder_path_str).relative_to(root))
+                    if relative_path == ".":
+                        relative_path = "."
+
+                    # Collect file info
+                    file_paths: list[str] = []
+                    files_info: list[dict[str, Any]] = []
+                    folder_size = 0
+                    for mcap_path in sorted(mcap_paths, key=lambda p: p.name):
+                        stat = mcap_path.stat()
+                        file_paths.append(str(mcap_path))
+                        folder_size += stat.st_size
+                        files_info.append({
+                            "path": str(mcap_path),
+                            "filename": mcap_path.name,
+                            "size": stat.st_size,
+                            "mtime": stat.st_mtime,
+                            "relative_path": str(mcap_path.relative_to(root)),
+                        })
+
+                    # Pre-filter this batch for duplicates
+                    _, pre_stats = self.pre_filter_files(
+                        file_paths, s3_bucket, aws_profile, aws_region,
+                        cache_only=cache_only,
+                    )
+
+                    # Merge pre-filter results into file info
+                    prefilter_map: dict[str, bool] = {}
+                    for fs in pre_stats.get("file_statuses", []):
+                        prefilter_map[fs["path"]] = fs.get("already_uploaded", False)
+
+                    already_uploaded_count = 0
+                    for fi in files_info:
+                        fi["already_uploaded"] = prefilter_map.get(fi["path"], False)
+                        if fi["already_uploaded"]:
+                            already_uploaded_count += 1
+
+                    all_uploaded = already_uploaded_count == len(files_info) and len(files_info) > 0
+
+                    scanned = ScannedFolder(
+                        folder_path=folder_path_str,
+                        relative_path=relative_path,
+                        files=files_info,
+                        total_files=len(files_info),
+                        already_uploaded=already_uploaded_count,
+                        all_uploaded=all_uploaded,
+                    )
+
+                except Exception as e:
+                    relative_path = str(Path(folder_path_str).relative_to(root))
+                    scanned = ScannedFolder(
+                        folder_path=folder_path_str,
+                        relative_path=relative_path,
+                        files=[],
+                        error=str(e),
+                    )
+                    log.error(
+                        "scan",
+                        "scan_folder_error",
+                        f"Error scanning {folder_path_str}: {e}",
+                        {"job_id": job_id, "folder": folder_path_str, "error": str(e)},
+                    )
+
+                # Build folder dict for both storage and SSE
+                folder_dict = {
+                    "relative_path": scanned.relative_path,
+                    "files": scanned.files,
+                    "total_files": scanned.total_files,
+                    "already_uploaded": scanned.already_uploaded,
+                    "all_uploaded": scanned.all_uploaded,
+                    "error": scanned.error,
+                }
+
+                # Update running totals and store results
+                with scan_job.lock:
+                    scan_job.folders_scanned += 1
+                    scan_job.total_files_found += scanned.total_files
+                    scan_job.total_already_uploaded += scanned.already_uploaded
+                    scan_job.total_size += sum(f.get("size", 0) for f in scanned.files)
+                    scan_job.scanned_folders.append(folder_dict)
+
+                if progress_callback:
+                    progress_callback(job_id, {
+                        "type": "scan_folder_complete",
+                        "folder": folder_dict,
+                        "folders_scanned": scan_job.folders_scanned,
+                        "folders_total": scan_job.folders_total,
+                        "running_totals": {
+                            "total_files_found": scan_job.total_files_found,
+                            "total_already_uploaded": scan_job.total_already_uploaded,
+                            "total_size": scan_job.total_size,
+                        },
+                    })
+
+            # Terminal event
+            with scan_job.lock:
+                if scan_job.cancelled:
+                    scan_job.status = "cancelled"
+                else:
+                    scan_job.status = "completed"
+
+            if progress_callback:
+                progress_callback(job_id, {
+                    "type": "scan_complete",
+                    "status": scan_job.status,
+                    "folders_scanned": scan_job.folders_scanned,
+                    "folders_total": scan_job.folders_total,
+                    "total_files_found": scan_job.total_files_found,
+                    "total_already_uploaded": scan_job.total_already_uploaded,
+                    "total_size": scan_job.total_size,
+                })
+
+        except Exception as e:
+            scan_job.status = "failed"
+            log.error(
+                "scan",
+                "scan_job_failed",
+                f"Scan job {job_id} failed: {e}",
+                {"job_id": job_id, "error": str(e)},
+            )
+            if progress_callback:
+                progress_callback(job_id, {
+                    "type": "scan_complete",
+                    "status": "failed",
+                    "error": str(e),
+                })
+
     def get_active_jobs(self) -> list[UploadJob]:
         """Get all currently active (non-terminal) jobs."""
         active_statuses = {

From acc35749a7463bf113c56b422e44f56a65f8966d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 12:48:30 -0700
Subject: [PATCH 003/173] JS: Track folder/files/jobs in state

---
 app/static/js/modules/state.js | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/app/static/js/modules/state.js b/app/static/js/modules/state.js
index d2e9107..1febefd 100644
--- a/app/static/js/modules/state.js
+++ b/app/static/js/modules/state.js
@@ -36,6 +36,9 @@ const state = {
   /** @type {string | null} */
   scanFolderPath: null,
 
+  /** @type {string | null} */
+  scanJobId: null,
+
   /** Sort configuration for the review table */
   reviewSortConfig: { column: 'filename', ascending: true },
 
@@ -45,6 +48,18 @@ const state = {
   /** Sort configuration for the folder browser file table */
   browserFileSortConfig: { column: 'name', ascending: true },
 
+  /** @type {Array<{ relative_path: string, files: any[], total_files: number, already_uploaded: number, all_uploaded: boolean, error: string | null }>} */
+  browserScanResults: [],
+
+  /** @type {EventSource | null} Browser scan SSE connection (separate from main eventSource) */
+  browserScanEventSource: null,
+
+  /** @type {string | null} Browser scan job ID */
+  browserScanJobId: null,
+
+  /** Whether the browser scan has completed */
+  browserScanComplete: false,
+
   /** Log viewer filter state */
   logFilters: {
     /** @type {string | null} */ date: null,

From ec46e36f916cdae1af2b798f0962a4278ba797b2 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 12:49:45 -0700
Subject: [PATCH 004/173] JS: Add toggles/ui for file listing/upload checking

---
 app/static/js/modules/folder-browser.js | 533 ++++++++++++++++++++----
 app/static/js/modules/upload-control.js |  10 +
 app/static/js/modules/upload-init.js    |  21 +-
 3 files changed, 486 insertions(+), 78 deletions(-)

diff --git a/app/static/js/modules/folder-browser.js b/app/static/js/modules/folder-browser.js
index 55c0102..42706ac 100644
--- a/app/static/js/modules/folder-browser.js
+++ b/app/static/js/modules/folder-browser.js
@@ -190,15 +190,16 @@ export async function loadFolderBrowser(path, isRetry = false) {
           ...data.folders.map(
             (/** @type {{ name: string, path: string, mcap_count: number }} */ folder) => `
                         <div class="px-6 py-3 flex items-center justify-between cursor-pointer hover:bg-gray-50"
-                             data-action="navigate-folder" data-path="${folder.path}">
+                             data-action="navigate-folder" data-path="${folder.path}"
+                             data-folder-name="${folder.name}">
                             <div class="flex items-center">
                                 ${folderIcon()}
                                 <span class="text-sm font-medium text-gray-900">${folder.name}</span>
                             </div>
                             ${
                               folder.mcap_count > 0
-                                ? `<span class="text-xs text-gray-500" title="Direct files only, not including subfolders">${folder.mcap_count} mcap</span>`
-                                : ''
+                                ? `<span class="folder-mcap-badge text-xs text-gray-500" title="Direct files only, not including subfolders">${folder.mcap_count} mcap</span>`
+                                : '<span class="folder-mcap-badge text-xs text-gray-500"></span>'
                             }
                         </div>
                     `,
@@ -220,6 +221,9 @@ export async function loadFolderBrowser(path, isRetry = false) {
       state.browserFiles = [];
       hideEl('file-table-section');
     }
+
+    // Start background scan for upload status enrichment
+    startBrowserScan(data.current_path);
   } catch (error) {
     hideEl('folder-loading');
     showEl('folder-error');
@@ -228,9 +232,10 @@ export async function loadFolderBrowser(path, isRetry = false) {
 }
 
 /**
- * Select the current folder and scan for MCAP files.
+ * Select the current folder and populate Step 2 from stored browser scan data.
+ * The browser scan has already accumulated state.scanFileStatuses and state.scanFilePaths.
  */
-async function selectCurrentFolder() {
+function selectCurrentFolder() {
   const btn = /** @type {HTMLButtonElement | null} */ (
     document.getElementById('select-folder-btn')
   );
@@ -239,105 +244,441 @@ async function selectCurrentFolder() {
   const folderPath = btn.dataset.path;
   if (!folderPath) return;
 
-  btn.disabled = true;
-  const btnSpan = btn.querySelector('span');
-  if (btnSpan) btnSpan.textContent = 'Scanning...';
+  state.selectedFolderPath = folderPath;
+  state.scanFolderPath = folderPath;
+  localStorage.setItem('lastUploadFolder', folderPath);
 
-  try {
-    const data = await apiPost('/api/upload/scan-folder', { folder_path: folderPath });
+  // Transition to Step 2 — populate from stored browser scan data
+  showUploadSteps(2);
+  state.reviewSortConfig = { column: 'filename', ascending: true };
+
+  setText('selected-folder-path', folderPath);
+  setText('scan-total', String(state.scanFileStatuses.length));
+  setText('scan-total-volume', formatBytes(state.scanTotalSize));
+  const uploadedCount = state.scanFileStatuses.filter(
+    (/** @type {any} */ f) => f.already_uploaded,
+  ).length;
+  setText('scan-already-uploaded', String(uploadedCount));
+
+  // Clear and populate review table from stored scan results
+  const tbody = document.getElementById('scan-file-list');
+  if (tbody) tbody.innerHTML = '';
+
+  for (const folder of state.browserScanResults) {
+    appendFolderToReviewTable(folder);
+  }
 
-    if (data.total_count === 0) {
-      showNotification('No MCAP files found in this folder', 'error');
-      return;
+  // Hide scan progress (scan already done), enable continue button
+  hideEl('scan-progress-container');
+  const continueBtn = /** @type {HTMLButtonElement | null} */ (
+    document.getElementById('continue-upload-btn')
+  );
+  if (continueBtn) {
+    continueBtn.disabled = state.scanFilePaths.length === 0;
+  }
+
+  const hideUploadedCheckbox = /** @type {HTMLInputElement | null} */ (
+    document.getElementById('scan-hide-uploaded')
+  );
+  if (hideUploadedCheckbox) {
+    hideUploadedCheckbox.checked = false;
+    hideUploadedCheckbox.onchange = () => applyScanFileFilter();
+  }
+
+  const hideCompletedFoldersCheckbox = /** @type {HTMLInputElement | null} */ (
+    document.getElementById('scan-hide-completed-folders')
+  );
+  if (hideCompletedFoldersCheckbox) {
+    hideCompletedFoldersCheckbox.checked = false;
+    hideCompletedFoldersCheckbox.onchange = () => applyScanFileFilter();
+  }
+
+  hideEl('folder-browser-panel');
+  showEl('scan-results-section');
+}
+
+/**
+ * Green checkmark SVG for fully-uploaded folders.
+ * @returns {string}
+ */
+function checkmarkIcon() {
+  return '<svg class="h-4 w-4 text-green-500 inline-block ml-1" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7" /></svg>';
+}
+
+/**
+ * Start a background cache-only scan for the current folder to enrich
+ * folder rows with upload status. Called automatically after navigation.
+ * @param {string} folderPath
+ */
+async function startBrowserScan(folderPath) {
+  // Cancel any existing browser scan
+  if (state.browserScanJobId) {
+    try {
+      await apiPost(`/api/upload/cancel/${state.browserScanJobId}`);
+    } catch (_error) {
+      // Scan may have already finished
     }
+  }
+  if (state.browserScanEventSource) {
+    state.browserScanEventSource.close();
+    state.browserScanEventSource = null;
+  }
 
-    state.selectedFolderPath = folderPath;
-    localStorage.setItem('lastUploadFolder', folderPath);
+  // Reset browser scan state
+  state.browserScanResults = [];
+  state.browserScanJobId = null;
+  state.browserScanComplete = false;
+  state.scanFileStatuses = [];
+  state.scanFilePaths = [];
+  state.scanTotalSize = 0;
 
-    const prefilterData = await apiPost('/api/upload/bulk-analyze', {
-      file_paths: data.files.map((/** @type {{ path: string }} */ f) => f.path),
-      pre_filter_only: true,
+  // Running aggregation map: immediate child folder name → { totalFiles, alreadyUploaded }
+  /** @type {Map<string, { totalFiles: number, alreadyUploaded: number }>} */
+  const folderAggregation = new Map();
+
+  // Root file aggregation (for files in the browsed folder itself)
+  let rootTotalFiles = 0;
+  let rootAlreadyUploaded = 0;
+
+  // Disable Upload button until scan completes
+  const selectBtn = /** @type {HTMLButtonElement | null} */ (
+    document.getElementById('select-folder-btn')
+  );
+  if (selectBtn) {
+    selectBtn.disabled = true;
+    const btnSpan = selectBtn.querySelector('span');
+    if (btnSpan) btnSpan.textContent = 'Scanning...';
+  }
+
+  // Show scan status bar
+  showEl('browser-scan-status');
+  const spinner = document.getElementById('browser-scan-spinner');
+  if (spinner) spinner.classList.remove('hidden');
+  setText('browser-scan-text', 'Scanning folders...');
+
+  // Wire up hide-uploaded toggle
+  const hideCheckbox = /** @type {HTMLInputElement | null} */ (
+    document.getElementById('browser-hide-uploaded')
+  );
+  if (hideCheckbox) {
+    hideCheckbox.onchange = () => applyBrowserHideUploaded(hideCheckbox.checked);
+  }
+
+  try {
+    const data = await apiPost('/api/upload/scan-folder-async', {
+      folder_path: folderPath,
+      cache_only: true,
     });
 
-    showScanResults(data, prefilterData.pre_filter_stats || {});
+    state.browserScanJobId = data.job_id;
+
+    // Connect SSE for browser scan progress
+    state.browserScanEventSource = new EventSource(`/api/upload/progress/${data.job_id}`);
+
+    state.browserScanEventSource.onmessage = (event) => {
+      const eventData = JSON.parse(event.data);
+
+      if (eventData.error) {
+        showNotification(eventData.error, 'error');
+        closeBrowserScan();
+        enableUploadButton(folderPath);
+        return;
+      }
+
+      if (eventData.type === 'scan_started') {
+        setText('browser-scan-text', `Scanning 0 of ${eventData.folders_total} folders...`);
+      }
+
+      if (eventData.type === 'scan_folder_complete') {
+        const folder = eventData.folder;
+        const totals = eventData.running_totals;
+
+        // Store result
+        state.browserScanResults.push(folder);
+        state.scanTotalSize = totals.total_size;
+
+        // Accumulate file statuses and paths
+        for (const file of folder.files) {
+          state.scanFileStatuses.push(file);
+          if (!file.already_uploaded) {
+            state.scanFilePaths.push(file.path);
+          }
+        }
+
+        // Determine which immediate child this leaf folder belongs to
+        if (folder.relative_path === '.') {
+          // Root folder files
+          rootTotalFiles += folder.total_files;
+          rootAlreadyUploaded += folder.already_uploaded;
+          updateRootUploadStatus(rootTotalFiles, rootAlreadyUploaded);
+        } else {
+          // Extract the first path component
+          const firstSlash = folder.relative_path.indexOf('/');
+          const immediateChild =
+            firstSlash >= 0 ? folder.relative_path.substring(0, firstSlash) : folder.relative_path;
+
+          const existing = folderAggregation.get(immediateChild) || {
+            totalFiles: 0,
+            alreadyUploaded: 0,
+          };
+          existing.totalFiles += folder.total_files;
+          existing.alreadyUploaded += folder.already_uploaded;
+          folderAggregation.set(immediateChild, existing);
+
+          // Update the matching folder row in the browser
+          updateFolderRowBadge(immediateChild, existing);
+        }
+
+        // Update status bar
+        setText(
+          'browser-scan-text',
+          `Scanning ${eventData.folders_scanned} of ${eventData.folders_total} folders...`,
+        );
+
+        // Update Upload button summary
+        updateUploadButtonSummary();
+      }
+
+      if (eventData.type === 'scan_complete') {
+        closeBrowserScan();
+        state.browserScanComplete = true;
+
+        // Hide spinner, show final status
+        if (spinner) spinner.classList.add('hidden');
+
+        const totalFiles = state.scanFileStatuses.length;
+        const alreadyUploaded = state.scanFileStatuses.filter(
+          (/** @type {any} */ f) => f.already_uploaded,
+        ).length;
+        const toUpload = totalFiles - alreadyUploaded;
+
+        if (totalFiles === 0) {
+          setText('browser-scan-text', 'No MCAP files found in subfolders.');
+          enableUploadButton(folderPath);
+        } else if (toUpload === 0) {
+          setText('browser-scan-text', `All ${totalFiles} files already uploaded.`);
+          enableUploadButton(folderPath, true);
+        } else {
+          setText(
+            'browser-scan-text',
+            `Scan complete: ${toUpload} to upload, ${alreadyUploaded} already uploaded.`,
+          );
+          enableUploadButton(folderPath);
+        }
+      }
+    };
+
+    state.browserScanEventSource.onerror = () => {
+      closeBrowserScan();
+      enableUploadButton(folderPath);
+    };
   } catch (error) {
     showNotification(/** @type {Error} */ (error).message, 'error');
-  } finally {
-    btn.disabled = false;
-    const resetSpan = btn.querySelector('span');
-    if (resetSpan) resetSpan.textContent = 'Upload This Folder';
+    closeBrowserScan();
+    enableUploadButton(folderPath);
   }
 }
 
 /**
- * Show scan results UI with sortable review table.
- * @param {any} scanData
- * @param {any} prefilterStats
+ * Close the browser scan SSE connection.
  */
-function showScanResults(scanData, prefilterStats) {
-  showUploadSteps(2);
+function closeBrowserScan() {
+  if (state.browserScanEventSource) {
+    state.browserScanEventSource.close();
+    state.browserScanEventSource = null;
+  }
+}
 
-  // Store folder path for relative path computation
-  state.scanFolderPath = scanData.folder_path;
-  state.scanTotalSize = scanData.total_size || 0;
+/**
+ * Re-enable the Upload button after scan completes.
+ * @param {string} folderPath
+ * @param {boolean} [allUploaded] - If true, keep button disabled (nothing to upload)
+ */
+function enableUploadButton(folderPath, allUploaded = false) {
+  const selectBtn = /** @type {HTMLButtonElement | null} */ (
+    document.getElementById('select-folder-btn')
+  );
+  if (!selectBtn) return;
 
-  setText('selected-folder-path', scanData.folder_path);
-  setText('scan-total', scanData.total_count);
-  setText('scan-total-volume', formatBytes(state.scanTotalSize));
-  setText('scan-already-uploaded', prefilterStats.cache_skipped || 0);
-
-  // Merge scan data files with prefilter statuses
-  const fileStatuses = prefilterStats.file_statuses || [];
-  /** @type {Map<string, any>} */
-  const prefilterMap = new Map();
-  for (const fs of fileStatuses) {
-    prefilterMap.set(fs.path, fs);
+  if (allUploaded) {
+    selectBtn.disabled = true;
+    const btnSpan = selectBtn.querySelector('span');
+    if (btnSpan) btnSpan.textContent = 'All Files Uploaded';
+  } else {
+    selectBtn.disabled = false;
+    selectBtn.dataset.path = folderPath;
+    updateUploadButtonSummary();
   }
+}
 
-  /** @type {Array<any>} */
-  const mergedStatuses = [];
-  for (const scanFile of scanData.files) {
-    const pf = prefilterMap.get(scanFile.path);
-    mergedStatuses.push({
-      path: scanFile.path,
-      filename: scanFile.filename,
-      size: scanFile.size,
-      mtime: scanFile.mtime || 0,
-      relative_path: scanFile.relative_path || scanFile.filename,
-      already_uploaded: pf ? pf.already_uploaded : false,
-    });
+/**
+ * Update the Upload button label and summary text based on scan data.
+ */
+function updateUploadButtonSummary() {
+  const toUploadCount = state.scanFilePaths.length;
+  const totalCount = state.scanFileStatuses.length;
+  const uploadedCount = totalCount - toUploadCount;
+
+  const selectBtn = /** @type {HTMLButtonElement | null} */ (
+    document.getElementById('select-folder-btn')
+  );
+  if (selectBtn) {
+    const btnSpan = selectBtn.querySelector('span');
+    if (btnSpan) {
+      if (toUploadCount > 0) {
+        btnSpan.textContent = `Upload ${toUploadCount} Files`;
+      } else if (totalCount > 0) {
+        btnSpan.textContent = 'All Files Uploaded';
+      } else {
+        btnSpan.textContent = 'Upload This Folder';
+      }
+    }
   }
 
-  state.scanFilePaths = mergedStatuses
-    .filter((/** @type {any} */ f) => !f.already_uploaded)
-    .map((/** @type {any} */ f) => f.path);
+  // Update bottom summary text
+  if (totalCount > 0) {
+    const sizeToUpload = state.scanFileStatuses
+      .filter((/** @type {any} */ f) => !f.already_uploaded)
+      .reduce((/** @type {number} */ sum, /** @type {any} */ f) => sum + f.size, 0);
+    if (toUploadCount > 0) {
+      setText(
+        'folder-select-summary',
+        `${toUploadCount} of ${totalCount} files to upload (${formatBytes(sizeToUpload)}). ${uploadedCount} already uploaded.`,
+      );
+    } else {
+      setText('folder-select-summary', `All ${totalCount} files are already uploaded.`);
+    }
+  }
+}
 
-  state.scanFileStatuses = mergedStatuses;
-  state.reviewSortConfig = { column: 'filename', ascending: true };
+/**
+ * Update a folder row's badge with scan results.
+ * @param {string} folderName
+ * @param {{ totalFiles: number, alreadyUploaded: number }} stats
+ */
+function updateFolderRowBadge(folderName, stats) {
+  const folderList = document.getElementById('folder-list');
+  if (!folderList) return;
 
-  renderReviewTable(mergedStatuses);
+  const row = folderList.querySelector(`[data-folder-name="${CSS.escape(folderName)}"]`);
+  if (!row) return;
 
-  const hideUploadedCheckbox = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('scan-hide-uploaded')
-  );
-  if (hideUploadedCheckbox) {
-    hideUploadedCheckbox.checked = false;
-    hideUploadedCheckbox.onchange = () => applyScanFileFilter();
+  const badge = row.querySelector('.folder-mcap-badge');
+  if (!badge) return;
+
+  const allUploaded = stats.alreadyUploaded === stats.totalFiles && stats.totalFiles > 0;
+
+  if (allUploaded) {
+    badge.innerHTML = `${stats.totalFiles} mcap (${stats.alreadyUploaded} uploaded) ${checkmarkIcon()}`;
+    row.classList.add('bg-green-50');
+    /** @type {HTMLElement} */ (row).dataset.allUploaded = 'true';
+  } else if (stats.alreadyUploaded > 0) {
+    badge.textContent = `${stats.totalFiles} mcap (${stats.alreadyUploaded} uploaded)`;
+  } else {
+    badge.textContent = `${stats.totalFiles} mcap`;
   }
+}
 
-  const continueBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('continue-upload-btn')
-  );
-  if (continueBtn) {
-    continueBtn.disabled = state.scanFileStatuses.length === 0;
+/**
+ * Update the root upload status in the MCAP count info bar.
+ * @param {number} totalFiles
+ * @param {number} alreadyUploaded
+ */
+function updateRootUploadStatus(totalFiles, alreadyUploaded) {
+  const statusEl = document.getElementById('browser-root-upload-status');
+  if (!statusEl) return;
+
+  if (alreadyUploaded === totalFiles && totalFiles > 0) {
+    statusEl.innerHTML = `<span class="text-green-600">(${alreadyUploaded} uploaded) ${checkmarkIcon()}</span>`;
+  } else if (alreadyUploaded > 0) {
+    statusEl.innerHTML = `<span class="text-gray-600">(${alreadyUploaded} of ${totalFiles} uploaded)</span>`;
   }
+}
 
-  hideEl('folder-browser-panel');
-  showEl('scan-results-section');
+/**
+ * Toggle visibility of fully-uploaded folder rows in the browser.
+ * @param {boolean} hide
+ */
+function applyBrowserHideUploaded(hide) {
+  const folderList = document.getElementById('folder-list');
+  if (!folderList) return;
+
+  const rows = folderList.querySelectorAll('[data-folder-name]');
+  for (const row of rows) {
+    if (hide && /** @type {HTMLElement} */ (row).dataset.allUploaded === 'true') {
+      /** @type {HTMLElement} */ (row).classList.add('hidden');
+    } else {
+      /** @type {HTMLElement} */ (row).classList.remove('hidden');
+    }
+  }
+}
+
+/**
+ * Append a scanned folder's results to the review table incrementally.
+ * @param {{ relative_path: string, files: any[], total_files: number, already_uploaded: number, all_uploaded: boolean, error: string | null }} folderData
+ */
+function appendFolderToReviewTable(folderData) {
+  const tbody = document.getElementById('scan-file-list');
+  if (!tbody) return;
+
+  const folderLabel = folderData.relative_path === '.' ? '(root)' : folderData.relative_path;
+  const uploadedSummary = `${folderData.already_uploaded}/${folderData.total_files} uploaded`;
+
+  // Build folder header row
+  const headerHtml = `
+    <tr class="bg-gray-100 ${folderData.all_uploaded ? 'folder-all-uploaded' : ''}"
+        data-folder-header
+        data-all-uploaded="${folderData.all_uploaded}">
+      <td colspan="5" class="px-4 py-2">
+        <div class="flex items-center justify-between">
+          <div class="flex items-center">
+            ${folderIcon('h-4 w-4 text-nlr-yellow mr-2')}
+            <span class="text-sm font-medium text-gray-700">${folderLabel}</span>
+            ${folderData.all_uploaded ? checkmarkIcon() : ''}
+          </div>
+          <div class="flex items-center space-x-2">
+            <span class="text-xs text-gray-500">${uploadedSummary}</span>
+            ${folderData.error ? `<span class="text-xs text-red-600 bg-red-100 px-2 py-0.5 rounded-full">Error: ${folderData.error}</span>` : ''}
+          </div>
+        </div>
+      </td>
+    </tr>
+  `;
+
+  // Build file rows under this folder
+  let fileRowsHtml = '';
+  for (const file of folderData.files) {
+    const dirPath = getDirectoryPart(file.relative_path);
+    fileRowsHtml += `
+      <tr class="${file.already_uploaded ? 'bg-yellow-50' : ''}"
+          data-already-uploaded="${file.already_uploaded}">
+        <td class="pl-8 pr-4 py-3">
+          <span class="text-sm ${file.already_uploaded ? 'text-gray-500' : 'text-gray-900'} truncate block" title="${file.filename}">
+            ${file.filename}
+          </span>
+        </td>
+        <td class="px-4 py-3">
+          <span class="text-sm text-gray-500 truncate block" title="${dirPath}">${dirPath || '.'}</span>
+        </td>
+        <td class="px-4 py-3 whitespace-nowrap text-sm text-gray-500">${formatMtime(file.mtime)}</td>
+        <td class="px-4 py-3 whitespace-nowrap text-sm text-gray-500">${formatBytes(file.size)}</td>
+        <td class="px-4 py-3 whitespace-nowrap">
+          <span class="px-2 py-1 text-xs rounded-full ${file.already_uploaded ? 'bg-yellow-100 text-yellow-800' : 'bg-green-100 text-green-800'}">
+            ${file.already_uploaded ? 'Uploaded' : 'To Upload'}
+          </span>
+        </td>
+      </tr>
+    `;
+  }
+
+  tbody.insertAdjacentHTML('beforeend', headerHtml + fileRowsHtml);
+
+  // Apply current filter
+  applyScanFileFilter();
 }
 
 /**
- * Render the sortable review table body.
+ * Render the sortable review table body (flat view, used for re-sorting).
  * @param {any[]} fileStatuses
  */
 function renderReviewTable(fileStatuses) {
@@ -422,12 +763,50 @@ function applyScanFileFilter() {
     document.getElementById('scan-hide-uploaded')
   );
   const hideUploaded = hideUploadedEl?.checked || false;
+
+  const hideCompletedFoldersEl = /** @type {HTMLInputElement | null} */ (
+    document.getElementById('scan-hide-completed-folders')
+  );
+  const hideCompletedFolders = hideCompletedFoldersEl?.checked || false;
+
   const tbody = document.getElementById('scan-file-list');
   if (!tbody) return;
 
-  const rows = tbody.querySelectorAll('[data-already-uploaded]');
-  for (const row of rows) {
-    if (hideUploaded && /** @type {HTMLElement} */ (row).dataset.alreadyUploaded === 'true') {
+  // Determine which folder headers are for completed folders
+  /** @type {Set<Element>} */
+  const hiddenFolderHeaders = new Set();
+
+  // First pass: process folder headers
+  const folderHeaders = tbody.querySelectorAll('[data-folder-header]');
+  for (const header of folderHeaders) {
+    if (
+      hideCompletedFolders &&
+      /** @type {HTMLElement} */ (header).dataset.allUploaded === 'true'
+    ) {
+      header.classList.add('hidden');
+      hiddenFolderHeaders.add(header);
+    } else {
+      header.classList.remove('hidden');
+    }
+  }
+
+  // Second pass: process file rows
+  // For each file row, find its parent folder header (the nearest preceding [data-folder-header])
+  const allRows = /** @type {NodeListOf<HTMLElement>} */ (tbody.querySelectorAll('tr'));
+  /** @type {Element | null} */
+  let currentFolderHeader = null;
+
+  for (const row of allRows) {
+    if (row.hasAttribute('data-folder-header')) {
+      currentFolderHeader = row;
+      continue;
+    }
+
+    // This is a file row
+    const isUploaded = row.dataset.alreadyUploaded === 'true';
+    const inHiddenFolder = currentFolderHeader && hiddenFolderHeaders.has(currentFolderHeader);
+
+    if (inHiddenFolder || (hideUploaded && isUploaded)) {
       row.classList.add('hidden');
     } else {
       row.classList.remove('hidden');
diff --git a/app/static/js/modules/upload-control.js b/app/static/js/modules/upload-control.js
index 62c107e..40d1b80 100644
--- a/app/static/js/modules/upload-control.js
+++ b/app/static/js/modules/upload-control.js
@@ -9,6 +9,15 @@ import state from './state.js';
 import { hideUploadSteps } from './stepper.js';
 
 export async function cancelUpload() {
+  // Cancel scan job if active
+  if (state.scanJobId) {
+    try {
+      await apiPost(`/api/upload/cancel/${state.scanJobId}`);
+    } catch (_error) {
+      // Scan may have already finished
+    }
+  }
+
   if (!state.currentJobId) return;
 
   try {
@@ -41,4 +50,5 @@ export function resetUpload() {
   state.scanFileStatuses = [];
   state.scanTotalSize = 0;
   state.scanFolderPath = null;
+  state.scanJobId = null;
 }
diff --git a/app/static/js/modules/upload-init.js b/app/static/js/modules/upload-init.js
index f952c20..28855ba 100644
--- a/app/static/js/modules/upload-init.js
+++ b/app/static/js/modules/upload-init.js
@@ -1,4 +1,5 @@
 import { checkForActiveJob } from './analysis.js';
+import { apiPost } from './api.js';
 import { hideEl, showEl } from './dom.js';
 import { initFolderBrowser, showConfirmModal, startCombinedUpload } from './folder-browser.js';
 /**
@@ -25,10 +26,28 @@ export function initUpload() {
   document.getElementById('continue-upload-btn')?.addEventListener('click', showConfirmModal);
   document.getElementById('confirm-upload-btn')?.addEventListener('click', startCombinedUpload);
 
-  document.getElementById('cancel-scan-btn')?.addEventListener('click', () => {
+  document.getElementById('cancel-scan-btn')?.addEventListener('click', async () => {
+    // Cancel active scan job if running
+    if (state.scanJobId) {
+      try {
+        await apiPost(`/api/upload/cancel/${state.scanJobId}`);
+      } catch (_error) {
+        // Scan may have already finished
+      }
+      if (state.eventSource) {
+        state.eventSource.close();
+        state.eventSource = null;
+      }
+      state.scanJobId = null;
+    }
+
     hideEl('scan-results-section');
     showEl('folder-browser-panel');
     state.selectedFolderPath = null;
+    state.scanFilePaths = [];
+    state.scanFileStatuses = [];
+    state.scanTotalSize = 0;
+    state.scanFolderPath = null;
     setUploadStep(1);
   });
 }

From 789e6306a992baa693281a9b2dd9753c71310826 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:54:40 -0700
Subject: [PATCH 005/173] Routes: Send less to browser for upload

---
 app/routes/upload.py | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/app/routes/upload.py b/app/routes/upload.py
index 326606a..b6e76e0 100644
--- a/app/routes/upload.py
+++ b/app/routes/upload.py
@@ -128,7 +128,6 @@ def run_analysis() -> None:
             "job_id": job.job_id,
             "status": "analyzing",
             "total_files": len(job.files),
-            "files": [f.to_dict() for f in job.files],
         }
     ), 202
 
@@ -161,8 +160,11 @@ def start_upload(job_id: str) -> tuple[Response, int]:
             skip_duplicates = data.get("skip_duplicates", True)
 
     def progress_callback(job: UploadJob) -> None:
-        """Send progress updates via SSE."""
-        send_sse_event(job.job_id, job.to_dict())
+        """Send progress updates via SSE — lightweight during upload, full at completion."""
+        if job.status in (UploadStatus.COMPLETED, UploadStatus.FAILED, UploadStatus.CANCELLED):
+            send_sse_event(job.job_id, job.to_dict())
+        else:
+            send_sse_event(job.job_id, job.to_progress_dict())
 
     # Start upload in background thread
     def run_upload() -> None:
@@ -206,7 +208,14 @@ def generate() -> Generator[str, None, None]:
             job = manager.get_job(job_id)
             scan_job = manager.get_scan_job(job_id) if not job else None
             if job:
-                yield f"data: {json.dumps(job.to_dict())}\n\n"
+                if job.status in (
+                    UploadStatus.COMPLETED,
+                    UploadStatus.FAILED,
+                    UploadStatus.CANCELLED,
+                ):
+                    yield f"data: {json.dumps(job.to_dict())}\n\n"
+                else:
+                    yield f"data: {json.dumps(job.to_progress_dict())}\n\n"
             elif scan_job:
                 yield f"data: {json.dumps({'type': 'scan_initial', 'status': scan_job.status})}\n\n"
 
@@ -530,8 +539,11 @@ def bulk_analyze() -> tuple[Response, int]:
     analysis_progress_callback = _make_analysis_callback(job.job_id)
 
     def upload_progress_callback(job: UploadJob) -> None:
-        """Send upload progress updates via SSE."""
-        send_sse_event(job.job_id, job.to_dict())
+        """Send upload progress updates via SSE — lightweight during upload, full at completion."""
+        if job.status in (UploadStatus.COMPLETED, UploadStatus.FAILED, UploadStatus.CANCELLED):
+            send_sse_event(job.job_id, job.to_dict())
+        else:
+            send_sse_event(job.job_id, job.to_progress_dict())
 
     # Start analysis in background thread
     def run_bulk_analysis() -> None:
@@ -586,6 +598,5 @@ def run_bulk_analysis() -> None:
             "total_files": len(job.files),
             "pre_filter_stats": pre_filter_stats,
             "auto_upload": auto_upload,
-            "files": [f.to_dict() for f in job.files],
         }
     ), 202

From 59c942987f17d28b454ec87a41b5d3d346a1b9d3 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:55:16 -0700
Subject: [PATCH 006/173] Templates; Add more columns to tables in place of
 more rows

---
 app/templates/index.html | 44 ++++++++++++++++++++++++++--------------
 1 file changed, 29 insertions(+), 15 deletions(-)

diff --git a/app/templates/index.html b/app/templates/index.html
index 0444aa1..4549e2f 100644
--- a/app/templates/index.html
+++ b/app/templates/index.html
@@ -233,20 +233,20 @@ <h2 class="text-lg font-semibold text-gray-900">Review Selected Files</h2>
                 <table class="w-full divide-y divide-gray-200 table-fixed">
                     <thead class="bg-gray-50">
                         <tr>
-                            <th class="w-1/4 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100" data-sort="filename">
-                                Filename <span class="sort-indicator"></span>
+                            <th class="w-1/4 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
+                                Filename
                             </th>
-                            <th class="w-1/4 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100" data-sort="path">
-                                Path <span class="sort-indicator"></span>
+                            <th class="w-1/4 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
+                                Path
                             </th>
-                            <th class="w-1/6 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100" data-sort="mtime">
-                                Date Modified <span class="sort-indicator"></span>
+                            <th class="w-1/6 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
+                                Date Modified
                             </th>
-                            <th class="w-20 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100" data-sort="size">
-                                Size <span class="sort-indicator"></span>
+                            <th class="w-20 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
+                                Size
                             </th>
-                            <th class="w-24 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100" data-sort="status">
-                                Status <span class="sort-indicator"></span>
+                            <th class="w-24 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
+                                Status
                             </th>
                         </tr>
                     </thead>
@@ -293,9 +293,18 @@ <h2 class="text-lg font-semibold text-gray-900">Upload Progress</h2>
                 </div>
             </div>
 
-            <!-- File Status List -->
-            <div id="upload-file-list" class="divide-y divide-gray-200 max-h-96 overflow-y-auto">
-                <!-- File progress items will be inserted here -->
+            <!-- Compact Status Counters -->
+            <div id="upload-status-counters" class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center space-x-4 text-sm">
+                <span class="text-blue-600"><span class="inline-block w-2 h-2 bg-blue-500 rounded-full mr-1 animate-pulse"></span> <span id="upload-count-active">0</span> active</span>
+                <span class="text-green-600">&#10003; <span id="upload-count-completed">0</span> completed</span>
+                <span class="text-yellow-600">&#9193; <span id="upload-count-skipped">0</span> skipped</span>
+                <span class="text-red-600">&#10007; <span id="upload-count-failed">0</span> failed</span>
+                <span class="text-gray-500">&#9203; <span id="upload-count-queued">0</span> queued</span>
+            </div>
+
+            <!-- Active Uploads (only currently processing files, max ~4-8) -->
+            <div id="upload-active-list" class="divide-y divide-gray-200">
+                <!-- Only actively uploading/analyzing files appear here -->
             </div>
         </div>
     </div>
@@ -357,10 +366,15 @@ <h2 class="text-lg font-semibold text-gray-900">Upload Summary</h2>
                 </div>
             </div>
 
-            <!-- File Details Table -->
+            <!-- File Details Table (paginated) -->
             <div class="border-t border-gray-200">
-                <div class="px-6 py-3 bg-gray-50 border-b border-gray-200">
+                <div class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center justify-between">
                     <span class="text-sm font-medium text-gray-700">File Details</span>
+                    <div id="completion-pagination" class="flex items-center space-x-2 text-sm">
+                        <button id="completion-prev-btn" class="px-3 py-1 bg-gray-200 rounded hover:bg-gray-300 disabled:opacity-50 disabled:cursor-not-allowed" disabled>Prev</button>
+                        <span id="completion-page-info" class="text-gray-600">Page 1 of 1</span>
+                        <button id="completion-next-btn" class="px-3 py-1 bg-gray-200 rounded hover:bg-gray-300 disabled:opacity-50 disabled:cursor-not-allowed" disabled>Next</button>
+                    </div>
                 </div>
                 <div class="overflow-x-auto">
                     <table class="w-full divide-y divide-gray-200">

From fd0ca2593d5b6deea117c699dd2747fd782cdb23 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:56:07 -0700
Subject: [PATCH 007/173] Service: Sends less data to browser from upload
 manager

---
 app/services/upload_manager.py | 37 +++++++++++++++++++++++++---------
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index dffcb1f..6cb3d6c 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -196,6 +196,33 @@ def average_upload_speed_mbps(self) -> float | None:
             return round(self.successfully_uploaded_bytes / duration / 1024 / 1024 * 8, 2)
         return None
 
+    def to_progress_dict(self) -> dict[str, Any]:
+        """Lightweight dict for SSE progress events.
+
+        Includes only job-level stats and currently active files (uploading/analyzing),
+        dropping the full 20K-file array that to_dict() includes.
+        """
+        active_files = [
+            f.to_dict()
+            for f in self.files
+            if f.status in (UploadStatus.UPLOADING, UploadStatus.ANALYZING)
+        ]
+        return {
+            "job_id": self.job_id,
+            "status": self.status.value,
+            "progress_percent": self.progress_percent,
+            "files_completed": self.files_completed,
+            "total_files": len(self.files),
+            "uploaded_bytes_formatted": format_file_size(self.uploaded_bytes),
+            "total_bytes_formatted": format_file_size(self.total_bytes),
+            "eta_seconds": self.eta_seconds,
+            "files_failed": self.files_failed,
+            "files_skipped": sum(1 for f in self.files if f.status == UploadStatus.SKIPPED),
+            "files_uploaded": sum(1 for f in self.files if f.status == UploadStatus.COMPLETED),
+            "cancelled": self.cancelled,
+            "files": active_files,
+        }
+
     def resolve_analysis_status(self) -> None:
         """Set job status based on file analysis results."""
         if any(f.status == UploadStatus.READY for f in self.files):
@@ -557,12 +584,6 @@ def analyze_job_async(
             {"job_id": job_id, "total_files": len(job.files)},
         )
 
-        # Keep files as PENDING; workers will mark ANALYZING when they start.
-        # Send initial callbacks so frontend knows the job started and can show queue.
-        if progress_callback:
-            for file_state in job.files:
-                progress_callback(job, file_state)
-
         # Create S3 client for duplicate checking
         try:
             s3_client = s3_service.create_s3_client(aws_profile, aws_region)
@@ -580,8 +601,6 @@ def analyze_job_async(
         cpu_workers = max(1, (os.cpu_count() or 4) - 1)
         for file_state in job.files:
             file_state.status = UploadStatus.ANALYZING
-            if progress_callback:
-                progress_callback(job, file_state)
 
         with ProcessPoolExecutor(max_workers=cpu_workers) as proc_executor:
             parse_futures = {
@@ -628,7 +647,7 @@ def analyze_job_async(
             for fut in as_completed(dup_futures):
                 file_state = dup_futures[fut]
                 try:
-                    future.result()
+                    fut.result()
                     file_state.status = UploadStatus.READY
                     log.info(
                         "analysis",

From 9d7fe1bbe7307e32c09e7508bf94c738c391e6ec Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:57:08 -0700
Subject: [PATCH 008/173] Analysis: Send smaller updates to the browser

---
 app/static/js/modules/analysis.js | 239 +++++++++++++++++-------------
 1 file changed, 134 insertions(+), 105 deletions(-)

diff --git a/app/static/js/modules/analysis.js b/app/static/js/modules/analysis.js
index acc4e18..d13ce1e 100644
--- a/app/static/js/modules/analysis.js
+++ b/app/static/js/modules/analysis.js
@@ -1,5 +1,9 @@
 /**
  * File analysis/validation and combined upload progress (Step 3).
+ *
+ * Performance: Instead of creating one DOM row per file (20K+ rows),
+ * we track status in a Map and only render active uploads (max ~4-8 rows).
+ * Status counters are maintained via simple arithmetic, not DOM scans.
  */
 import { apiGet } from './api.js';
 import { hideEl, setText, showEl } from './dom.js';
@@ -14,7 +18,7 @@ const ANALYSIS_WEIGHT = 70;
 const UPLOAD_WEIGHT = 30;
 
 /**
- * Cache of last-known status per filename to avoid redundant DOM rebuilds.
+ * Cache of last-known status per filename.
  * @type {Map<string, string>}
  */
 const fileRowStatusCache = new Map();
@@ -28,8 +32,19 @@ let rafScheduled = false;
 /** Pending overall progress data to flush. @type {any} */
 let pendingProgressData = null;
 
-/** Current phase of the upload flow: 'analysis' or 'upload'. */
-let currentPhase = 'analysis';
+/**
+ * Status counters — maintained via transitions, never DOM-scanned.
+ * @type {{ pending: number, analyzing: number, ready: number, uploading: number, completed: number, skipped: number, failed: number }}
+ */
+const counts = {
+  pending: 0,
+  analyzing: 0,
+  ready: 0,
+  uploading: 0,
+  completed: 0,
+  skipped: 0,
+  failed: 0,
+};
 
 /**
  * Reset internal state (call when starting a new job or resetting).
@@ -39,7 +54,24 @@ export function resetAnalysisState() {
   pendingFileUpdates.clear();
   pendingProgressData = null;
   rafScheduled = false;
-  currentPhase = 'analysis';
+
+  counts.pending = 0;
+  counts.analyzing = 0;
+  counts.ready = 0;
+  counts.uploading = 0;
+  counts.completed = 0;
+  counts.skipped = 0;
+  counts.failed = 0;
+}
+
+/**
+ * Initialize status counters for a new job.
+ * @param {number} totalFiles
+ */
+export function initStatusCounts(totalFiles) {
+  resetAnalysisState();
+  counts.pending = totalFiles;
+  updateCounterDisplay();
 }
 
 /**
@@ -115,6 +147,7 @@ export function connectCombinedProgressStream(jobId) {
       // Set total from the first event that carries it
       if (data.total_files && analysisTotal === 0) {
         analysisTotal = data.total_files;
+        counts.pending = analysisTotal;
         setText('files-total', data.total_files);
       }
 
@@ -123,7 +156,7 @@ export function connectCombinedProgressStream(jobId) {
         analysisCompleted++;
       }
 
-      // Update progress bar for analysis phase (use float, let CSS transition smooth it)
+      // Update progress bar for analysis phase
       if (analysisTotal > 0) {
         const percent = (analysisCompleted / analysisTotal) * ANALYSIS_WEIGHT;
         setProgressBar(percent);
@@ -143,7 +176,6 @@ export function connectCombinedProgressStream(jobId) {
 
     // Auto-upload starting
     if (data.type === 'auto_upload_starting') {
-      currentPhase = 'upload';
       setPhaseLabel('Uploading files...');
     }
 
@@ -222,18 +254,35 @@ function scheduleRaf() {
   }
 }
 
-/** Flush all pending updates in a single animation frame. */
+/**
+ * Flush all pending updates in a single animation frame.
+ * Updates status counters and active upload rows — no per-file DOM scan.
+ */
 function flushUpdates() {
   rafScheduled = false;
 
-  // Flush pending file row updates
-  for (const [, fileData] of pendingFileUpdates) {
-    updateUploadFileRow(fileData);
+  // Process all pending file updates: track status transitions and active files
+  for (const [filename, fileData] of pendingFileUpdates) {
+    const oldStatus = fileRowStatusCache.get(filename) || 'pending';
+    const newStatus = fileData.is_duplicate ? 'skipped' : fileData.status;
+
+    if (oldStatus !== newStatus) {
+      // Decrement old counter
+      if (oldStatus in counts) counts[/** @type {keyof counts} */ (oldStatus)]--;
+      // Increment new counter
+      if (newStatus in counts) counts[/** @type {keyof counts} */ (newStatus)]++;
+
+      fileRowStatusCache.set(filename, newStatus);
+    }
   }
+
+  // Update active upload rows (only currently uploading/analyzing files)
+  updateActiveRows();
+
   pendingFileUpdates.clear();
 
-  // Recompute queue positions after row updates
-  recomputeQueuePositions();
+  // Update status counter display
+  updateCounterDisplay();
 
   // Flush pending overall progress
   if (pendingProgressData) {
@@ -243,103 +292,90 @@ function flushUpdates() {
 }
 
 /**
- * Recompute "Queued (X of Y)" labels for pending/ready-queued files.
+ * Update the active upload rows — only render files that are currently
+ * uploading or analyzing (max ~4-8 rows instead of 20K).
  */
-function recomputeQueuePositions() {
-  const allRows = document.querySelectorAll('[data-upload-file]');
-  // Determine which statuses count as "queued" based on current phase
-  const queuedStatuses = currentPhase === 'upload' ? ['ready'] : ['pending'];
-
-  // First pass: count queued files
-  let totalQueued = 0;
-  for (const row of allRows) {
-    const filename = /** @type {HTMLElement} */ (row).getAttribute('data-upload-file');
-    const status = fileRowStatusCache.get(filename || '');
-    if (status && queuedStatuses.includes(status)) {
-      totalQueued++;
+function updateActiveRows() {
+  const container = document.getElementById('upload-active-list');
+  if (!container) return;
+
+  // Collect currently active files from pending updates
+  /** @type {any[]} */
+  const activeFiles = [];
+  for (const [, fileData] of pendingFileUpdates) {
+    if (fileData.status === 'uploading' || fileData.status === 'analyzing') {
+      activeFiles.push(fileData);
     }
   }
 
-  if (totalQueued === 0) return;
-
-  // Second pass: assign positions
-  let pos = 1;
-  for (const row of allRows) {
-    const filename = /** @type {HTMLElement} */ (row).getAttribute('data-upload-file');
-    const status = fileRowStatusCache.get(filename || '');
-    if (status && queuedStatuses.includes(status)) {
-      const label = row.querySelector('[data-queue-label]');
-      if (label) {
-        label.textContent =
-          currentPhase === 'upload'
-            ? `Queued for upload (${pos} of ${totalQueued})`
-            : `Queued (${pos} of ${totalQueued})`;
-      }
-      pos++;
+  // Also keep rows that are still active but weren't in this update batch
+  const existingRows = container.querySelectorAll('[data-upload-file]');
+  for (const row of existingRows) {
+    const filename = /** @type {HTMLElement} */ (row).getAttribute('data-upload-file') || '';
+    const currentStatus = fileRowStatusCache.get(filename);
+    if (currentStatus === 'uploading' || currentStatus === 'analyzing') {
+      // Keep it if not being replaced by a pending update
+      if (!pendingFileUpdates.has(filename)) continue;
+    } else {
+      // Status changed to non-active — remove row
+      row.remove();
     }
   }
-}
 
-/**
- * Update a single file row with minimal DOM changes.
- * Only rebuilds innerHTML on status transitions; for uploading progress,
- * just updates the bar width and percentage text to avoid resetting spinners.
- * @param {any} fileData
- */
-function updateUploadFileRow(fileData) {
-  const row = document.querySelector(`[data-upload-file="${fileData.filename}"]`);
-  if (!row) return;
-
-  const cachedStatus = fileRowStatusCache.get(fileData.filename);
-  const newStatus = fileData.is_duplicate ? `${fileData.status}:dup` : fileData.status;
-
-  // If status hasn't changed, only do micro-updates for uploading progress
-  if (cachedStatus === newStatus) {
-    if (fileData.status === 'uploading') {
-      const bar = /** @type {HTMLElement | null} */ (row.querySelector('[data-progress-bar]'));
-      if (bar) bar.style.width = `${fileData.progress_percent || 0}%`;
-      const label = row.querySelector('[data-progress-label]');
-      if (label) {
-        label.textContent =
-          fileData.progress_percent != null ? `${fileData.progress_percent.toFixed(0)}%` : '';
+  // Upsert active file rows
+  for (const fileData of activeFiles) {
+    const row = container.querySelector(`[data-upload-file="${CSS.escape(fileData.filename)}"]`);
+
+    if (row) {
+      // Existing row — micro-update for progress
+      if (fileData.status === 'uploading') {
+        const bar = /** @type {HTMLElement | null} */ (row.querySelector('[data-progress-bar]'));
+        if (bar) bar.style.width = `${fileData.progress_percent || 0}%`;
+        const label = row.querySelector('[data-progress-label]');
+        if (label) {
+          label.textContent =
+            fileData.progress_percent != null ? `${fileData.progress_percent.toFixed(0)}%` : '';
+        }
+      } else {
+        // Status changed (e.g., pending → analyzing) — rebuild
+        row.innerHTML = buildActiveRowHTML(fileData);
       }
+    } else {
+      // New active row
+      const div = document.createElement('div');
+      div.className = 'px-6 py-3 flex items-center justify-between';
+      div.setAttribute('data-upload-file', fileData.filename);
+      div.innerHTML = buildActiveRowHTML(fileData);
+      container.appendChild(div);
     }
-    return;
   }
 
-  // Status changed — full rebuild of the row
-  fileRowStatusCache.set(fileData.filename, newStatus);
-  row.innerHTML = buildFileRowHTML(fileData);
+  // Remove rows for files that completed/failed/skipped (no longer active)
+  for (const row of container.querySelectorAll('[data-upload-file]')) {
+    const filename = /** @type {HTMLElement} */ (row).getAttribute('data-upload-file') || '';
+    const status = fileRowStatusCache.get(filename);
+    if (status !== 'uploading' && status !== 'analyzing') {
+      row.remove();
+    }
+  }
 }
 
 /**
- * Build the full HTML for a file row.
+ * Build HTML for an active file row.
  * @param {any} fileData
  * @returns {string}
  */
-function buildFileRowHTML(fileData) {
+function buildActiveRowHTML(fileData) {
   let statusIcon = '';
   let statusText = '';
 
-  if (fileData.status === 'completed') {
-    statusIcon =
-      '<svg class="h-5 w-5 text-green-500" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7" /></svg>';
-    statusText = '<span class="text-xs text-green-600">Uploaded</span>';
-  } else if (fileData.status === 'failed') {
-    statusIcon =
-      '<svg class="h-5 w-5 text-red-500" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M6 18L18 6M6 6l12 12" /></svg>';
-    statusText = `<span class="text-xs text-red-600" title="${fileData.error_message || ''}">Failed</span>`;
-  } else if (fileData.status === 'skipped') {
-    statusIcon =
-      '<svg class="h-5 w-5 text-yellow-500" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 9l3 3m0 0l-3 3m3-3H8m13 0a9 9 0 11-18 0 9 9 0 0118 0z" /></svg>';
-    statusText = '<span class="text-xs text-yellow-600">Skipped</span>';
-  } else if (fileData.status === 'uploading') {
+  if (fileData.status === 'uploading') {
     statusIcon =
       '<svg class="spinner h-5 w-5 text-nlr-blue" fill="none" viewBox="0 0 24 24"><circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle><path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path></svg>';
     const pct = fileData.progress_percent != null ? `${fileData.progress_percent.toFixed(0)}%` : '';
     statusText = `
       <div class="flex items-center space-x-2">
-        <div class="w-16 bg-gray-200 rounded-full h-2">
+        <div class="w-20 bg-gray-200 rounded-full h-2">
           <div data-progress-bar class="bg-nlr-blue h-2 rounded-full transition-[width] duration-300 ease-out" style="width: ${fileData.progress_percent || 0}%"></div>
         </div>
         <span data-progress-label class="text-xs text-gray-500 w-8">${pct}</span>
@@ -348,27 +384,6 @@ function buildFileRowHTML(fileData) {
     statusIcon =
       '<svg class="spinner h-5 w-5 text-blue-500" fill="none" viewBox="0 0 24 24"><circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle><path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path></svg>';
     statusText = '<span class="text-xs text-blue-600">Validating</span>';
-  } else if (fileData.status === 'ready') {
-    if (fileData.is_duplicate) {
-      statusIcon =
-        '<svg class="h-5 w-5 text-yellow-500" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7" /></svg>';
-      statusText = '<span class="text-xs text-yellow-600">Duplicate</span>';
-    } else if (currentPhase === 'upload') {
-      // In upload phase, non-duplicate ready files are queued for upload
-      statusIcon =
-        '<div class="h-5 w-5 text-gray-400"><svg class="h-5 w-5 animate-pulse" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 8v4l3 3m6-3a9 9 0 11-18 0 9 9 0 0118 0z" /></svg></div>';
-      statusText = '<span data-queue-label class="text-xs text-gray-500">Queued for upload</span>';
-    } else {
-      statusIcon =
-        '<svg class="h-5 w-5 text-green-400" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 12l2 2 4-4" /></svg>';
-      statusText = '<span class="text-xs text-green-600">Validated</span>';
-    }
-  } else if (fileData.status === 'pending') {
-    statusIcon =
-      '<div class="h-5 w-5 text-gray-400"><svg class="h-5 w-5 animate-pulse" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 8v4l3 3m6-3a9 9 0 11-18 0 9 9 0 0118 0z" /></svg></div>';
-    statusText = '<span data-queue-label class="text-xs text-gray-500">Queued</span>';
-  } else {
-    statusText = `<span class="text-xs text-gray-400">${fileData.status || 'Unknown'}</span>`;
   }
 
   return `
@@ -383,6 +398,20 @@ function buildFileRowHTML(fileData) {
   `;
 }
 
+/**
+ * Update the status counter display from the counts object.
+ * O(1) — just setting text on 5 elements.
+ */
+function updateCounterDisplay() {
+  const active = counts.analyzing + counts.uploading;
+  const queued = counts.pending + counts.ready;
+  setText('upload-count-active', String(active));
+  setText('upload-count-completed', String(counts.completed));
+  setText('upload-count-skipped', String(counts.skipped));
+  setText('upload-count-failed', String(counts.failed));
+  setText('upload-count-queued', String(queued));
+}
+
 /**
  * @param {any} fileData
  * @returns {string}

From 8eb2a7588f3d268e9a14b4353ff4a6acc586db1b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:58:08 -0700
Subject: [PATCH 009/173] JS: Allow different truncation styles of folders

---
 app/static/js/modules/folder-browser.js | 201 +++++++++---------------
 1 file changed, 75 insertions(+), 126 deletions(-)

diff --git a/app/static/js/modules/folder-browser.js b/app/static/js/modules/folder-browser.js
index 42706ac..663a0c1 100644
--- a/app/static/js/modules/folder-browser.js
+++ b/app/static/js/modules/folder-browser.js
@@ -33,13 +33,13 @@ export async function initFolderBrowser() {
   document.getElementById('folder-quick-links')?.addEventListener('click', handleFolderNavClick);
   document.getElementById('folder-breadcrumb')?.addEventListener('click', handleFolderNavClick);
 
-  // Sort header click handler (Review table)
+  // Click handler for Review table (folder expand/collapse)
   const scanSection = document.getElementById('scan-results-section');
   if (scanSection) {
     scanSection.addEventListener('click', (e) => {
-      const th = /** @type {HTMLElement} */ (e.target).closest('[data-sort]');
-      if (th) {
-        sortReviewTable(/** @type {HTMLElement} */ (th).dataset.sort || 'filename');
+      const folderHeader = /** @type {HTMLElement} */ (e.target).closest('[data-folder-header]');
+      if (folderHeader) {
+        toggleFolderExpand(/** @type {HTMLTableRowElement} */ (folderHeader));
       }
     });
   }
@@ -264,8 +264,8 @@ function selectCurrentFolder() {
   const tbody = document.getElementById('scan-file-list');
   if (tbody) tbody.innerHTML = '';
 
-  for (const folder of state.browserScanResults) {
-    appendFolderToReviewTable(folder);
+  for (let i = 0; i < state.browserScanResults.length; i++) {
+    appendFolderToReviewTable(state.browserScanResults[i], i);
   }
 
   // Hide scan progress (scan already done), enable continue button
@@ -614,48 +614,83 @@ function applyBrowserHideUploaded(hide) {
 }
 
 /**
- * Append a scanned folder's results to the review table incrementally.
+ * Append a scanned folder as a collapsed summary row in the review table.
+ * File rows are only rendered on-demand when the folder header is expanded.
  * @param {{ relative_path: string, files: any[], total_files: number, already_uploaded: number, all_uploaded: boolean, error: string | null }} folderData
+ * @param {number} folderIndex - Index into state.browserScanResults
  */
-function appendFolderToReviewTable(folderData) {
+function appendFolderToReviewTable(folderData, folderIndex) {
   const tbody = document.getElementById('scan-file-list');
   if (!tbody) return;
 
   const folderLabel = folderData.relative_path === '.' ? '(root)' : folderData.relative_path;
-  const uploadedSummary = `${folderData.already_uploaded}/${folderData.total_files} uploaded`;
+  const toUpload = folderData.total_files - folderData.already_uploaded;
 
-  // Build folder header row
+  // Collapsed folder header only — no file rows (rendered on expand)
   const headerHtml = `
-    <tr class="bg-gray-100 ${folderData.all_uploaded ? 'folder-all-uploaded' : ''}"
+    <tr class="bg-gray-100 cursor-pointer hover:bg-gray-200 select-none ${folderData.all_uploaded ? 'folder-all-uploaded' : ''}"
         data-folder-header
-        data-all-uploaded="${folderData.all_uploaded}">
+        data-folder-idx="${folderIndex}"
+        data-all-uploaded="${folderData.all_uploaded}"
+        data-expanded="false">
       <td colspan="5" class="px-4 py-2">
         <div class="flex items-center justify-between">
           <div class="flex items-center">
+            <svg class="folder-chevron h-4 w-4 text-gray-400 mr-2 transition-transform flex-shrink-0" fill="none" viewBox="0 0 24 24" stroke="currentColor">
+              <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 5l7 7-7 7" />
+            </svg>
             ${folderIcon('h-4 w-4 text-nlr-yellow mr-2')}
             <span class="text-sm font-medium text-gray-700">${folderLabel}</span>
             ${folderData.all_uploaded ? checkmarkIcon() : ''}
           </div>
-          <div class="flex items-center space-x-2">
-            <span class="text-xs text-gray-500">${uploadedSummary}</span>
-            ${folderData.error ? `<span class="text-xs text-red-600 bg-red-100 px-2 py-0.5 rounded-full">Error: ${folderData.error}</span>` : ''}
+          <div class="flex items-center space-x-3">
+            <span class="text-xs text-gray-600">${folderData.total_files} files</span>
+            ${toUpload > 0 ? `<span class="text-xs font-medium text-green-700">${toUpload} to upload</span>` : ''}
+            ${folderData.already_uploaded > 0 ? `<span class="text-xs text-gray-500">${folderData.already_uploaded} uploaded</span>` : ''}
+            ${folderData.error ? `<span class="text-xs text-red-600 bg-red-100 px-2 py-0.5 rounded-full">Error</span>` : ''}
           </div>
         </div>
       </td>
     </tr>
   `;
 
-  // Build file rows under this folder
-  let fileRowsHtml = '';
-  for (const file of folderData.files) {
-    const dirPath = getDirectoryPart(file.relative_path);
-    fileRowsHtml += `
-      <tr class="${file.already_uploaded ? 'bg-yellow-50' : ''}"
-          data-already-uploaded="${file.already_uploaded}">
+  tbody.insertAdjacentHTML('beforeend', headerHtml);
+  applyScanFileFilter();
+}
+
+/**
+ * Toggle expand/collapse of a folder in the review table.
+ * @param {HTMLTableRowElement} headerRow
+ */
+function toggleFolderExpand(headerRow) {
+  const idx = Number.parseInt(headerRow.dataset.folderIdx || '0', 10);
+  const folderData = state.browserScanResults[idx];
+  if (!folderData) return;
+
+  const isExpanded = headerRow.dataset.expanded === 'true';
+  const chevron = headerRow.querySelector('.folder-chevron');
+
+  if (isExpanded) {
+    // Collapse: remove file rows after this header until next header
+    let next = headerRow.nextElementSibling;
+    while (next && !next.hasAttribute('data-folder-header')) {
+      const toRemove = next;
+      next = next.nextElementSibling;
+      toRemove.remove();
+    }
+    headerRow.dataset.expanded = 'false';
+    if (chevron) chevron.classList.remove('rotate-90');
+  } else {
+    // Expand: render file rows after this header using a DocumentFragment
+    const fragment = document.createDocumentFragment();
+    for (const file of folderData.files) {
+      const tr = document.createElement('tr');
+      tr.className = file.already_uploaded ? 'bg-yellow-50' : '';
+      tr.dataset.alreadyUploaded = String(file.already_uploaded);
+      const dirPath = getDirectoryPart(file.relative_path);
+      tr.innerHTML = `
         <td class="pl-8 pr-4 py-3">
-          <span class="text-sm ${file.already_uploaded ? 'text-gray-500' : 'text-gray-900'} truncate block" title="${file.filename}">
-            ${file.filename}
-          </span>
+          <span class="text-sm ${file.already_uploaded ? 'text-gray-500' : 'text-gray-900'} truncate block" title="${file.filename}">${file.filename}</span>
         </td>
         <td class="px-4 py-3">
           <span class="text-sm text-gray-500 truncate block" title="${dirPath}">${dirPath || '.'}</span>
@@ -667,76 +702,13 @@ function appendFolderToReviewTable(folderData) {
             ${file.already_uploaded ? 'Uploaded' : 'To Upload'}
           </span>
         </td>
-      </tr>
-    `;
-  }
-
-  tbody.insertAdjacentHTML('beforeend', headerHtml + fileRowsHtml);
-
-  // Apply current filter
-  applyScanFileFilter();
-}
-
-/**
- * Render the sortable review table body (flat view, used for re-sorting).
- * @param {any[]} fileStatuses
- */
-function renderReviewTable(fileStatuses) {
-  const tbody = document.getElementById('scan-file-list');
-  if (!tbody) return;
-
-  const { column, ascending } = state.reviewSortConfig;
-
-  const sorted = [...fileStatuses].sort((a, b) => {
-    let cmp = 0;
-    if (column === 'filename') {
-      cmp = a.filename.localeCompare(b.filename);
-    } else if (column === 'path') {
-      const aDir = getDirectoryPart(a.relative_path);
-      const bDir = getDirectoryPart(b.relative_path);
-      cmp = aDir.localeCompare(bDir);
-    } else if (column === 'mtime') {
-      cmp = (a.mtime || 0) - (b.mtime || 0);
-    } else if (column === 'size') {
-      cmp = a.size - b.size;
-    } else if (column === 'status') {
-      cmp = Number(a.already_uploaded) - Number(b.already_uploaded);
+      `;
+      fragment.appendChild(tr);
     }
-    return ascending ? cmp : -cmp;
-  });
-
-  tbody.innerHTML = sorted
-    .map((file) => {
-      const dirPath = getDirectoryPart(file.relative_path);
-
-      return `
-        <tr class="${file.already_uploaded ? 'bg-yellow-50' : ''}"
-            data-already-uploaded="${file.already_uploaded}">
-            <td class="px-4 py-3">
-                <span class="text-sm ${file.already_uploaded ? 'text-gray-500' : 'text-gray-900'} truncate block" title="${file.filename}">
-                    ${file.filename}
-                </span>
-            </td>
-            <td class="px-4 py-3">
-                <span class="text-sm text-gray-500 truncate block" title="${dirPath}">${dirPath || '.'}</span>
-            </td>
-            <td class="px-4 py-3 whitespace-nowrap text-sm text-gray-500">${formatMtime(file.mtime)}</td>
-            <td class="px-4 py-3 whitespace-nowrap text-sm text-gray-500">${formatBytes(file.size)}</td>
-            <td class="px-4 py-3 whitespace-nowrap">
-                <span class="px-2 py-1 text-xs rounded-full ${file.already_uploaded ? 'bg-yellow-100 text-yellow-800' : 'bg-green-100 text-green-800'}">
-                    ${file.already_uploaded ? 'Uploaded' : 'To Upload'}
-                </span>
-            </td>
-        </tr>
-    `;
-    })
-    .join('');
-
-  // Update sort indicators
-  updateSortIndicators('[data-sort]', '.sort-indicator', 'sort', column, ascending);
-
-  // Re-apply filter
-  applyScanFileFilter();
+    headerRow.after(fragment);
+    headerRow.dataset.expanded = 'true';
+    if (chevron) chevron.classList.add('rotate-90');
+  }
 }
 
 /**
@@ -749,15 +721,6 @@ function getDirectoryPart(relativePath) {
   return lastSlash >= 0 ? relativePath.substring(0, lastSlash) : '';
 }
 
-/**
- * Sort the review table by column.
- * @param {string} column
- */
-function sortReviewTable(column) {
-  toggleSort(state.reviewSortConfig, column);
-  renderReviewTable(state.scanFileStatuses);
-}
-
 function applyScanFileFilter() {
   const hideUploadedEl = /** @type {HTMLInputElement | null} */ (
     document.getElementById('scan-hide-uploaded')
@@ -974,30 +937,16 @@ function sortBrowserFileTable(column) {
 }
 
 /**
- * Initialize the upload file list with queued status.
+ * Initialize the upload view for a new job.
+ * Instead of creating 20K+ DOM rows, initialize status counters and
+ * clear the active upload area. Active files render on-demand.
  * @param {string[]} filePaths
  */
 function initUploadFileList(filePaths) {
-  const listEl = document.getElementById('upload-file-list');
-  if (!listEl) return;
-
-  const total = filePaths.length;
-  listEl.innerHTML = filePaths
-    .map((path, index) => {
-      const filename = path.split('/').pop() || path;
-      return `
-        <div class="px-6 py-3 flex items-center justify-between" data-upload-file="${filename}">
-            <div class="flex items-center space-x-3">
-                <div class="h-5 w-5 text-gray-400">
-                    <svg class="h-5 w-5 animate-pulse" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 8v4l3 3m6-3a9 9 0 11-18 0 9 9 0 0118 0z" />
-                    </svg>
-                </div>
-                <span class="text-sm text-gray-900">${filename}</span>
-            </div>
-            <span data-queue-label class="text-xs text-gray-500">Queued (${index + 1} of ${total})</span>
-        </div>
-      `;
-    })
-    .join('');
+  const activeList = document.getElementById('upload-active-list');
+  if (activeList) activeList.innerHTML = '';
+
+  // Initialize counters (all files start as "pending")
+  initStatusCounts(filePaths.length);
+  setText('files-total', String(filePaths.length));
 }

From 1a141b9d07a6d6640e232700ac38271d0ca903f7 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:58:40 -0700
Subject: [PATCH 010/173] Upload: Show at max 100 rows per page

---
 app/static/js/modules/upload-exec.js | 104 ++++++++++++++++++++++-----
 1 file changed, 85 insertions(+), 19 deletions(-)

diff --git a/app/static/js/modules/upload-exec.js b/app/static/js/modules/upload-exec.js
index a164da9..85736f8 100644
--- a/app/static/js/modules/upload-exec.js
+++ b/app/static/js/modules/upload-exec.js
@@ -1,5 +1,6 @@
 /**
  * Upload execution: progress tracking and completion summary.
+ * Completion table is paginated (100 rows per page) for 20K+ file performance.
  */
 import { hideEl, setText, showEl } from './dom.js';
 import { formatDuration, formatEta } from './formatters.js';
@@ -7,9 +8,14 @@ import { fileIcon } from './icons.js';
 import { showNotification } from './notify.js';
 import { setUploadStep } from './stepper.js';
 
+const COMPLETION_PAGE_SIZE = 100;
+
 /** @type {any} */
 let lastCompletedJob = null;
 
+/** Current page (0-indexed) of the completion table. */
+let completionPage = 0;
+
 /**
  * @param {any} job
  */
@@ -30,14 +36,20 @@ export function updateProgressUI(job) {
  */
 export function showCompletionSummary(job) {
   lastCompletedJob = job;
+  completionPage = 0;
   setUploadStep(4);
 
   hideEl('upload-section');
   showEl('completion-section');
 
-  const completed = job.files.filter((/** @type {any} */ f) => f.status === 'completed').length;
-  const skipped = job.files.filter((/** @type {any} */ f) => f.status === 'skipped').length;
-  const failed = job.files.filter((/** @type {any} */ f) => f.status === 'failed').length;
+  // Use pre-computed counts from backend (avoids 3 filter passes over 20K files)
+  const completed =
+    job.files_uploaded ??
+    job.files.filter((/** @type {any} */ f) => f.status === 'completed').length;
+  const skipped =
+    job.files_skipped ?? job.files.filter((/** @type {any} */ f) => f.status === 'skipped').length;
+  const failed =
+    job.files_failed ?? job.files.filter((/** @type {any} */ f) => f.status === 'failed').length;
 
   setText('completed-count', completed);
   setText('skipped-count', skipped);
@@ -49,23 +61,43 @@ export function showCompletionSummary(job) {
     job.average_upload_speed_mbps ? `${job.average_upload_speed_mbps} Mbps` : '-',
   );
 
-  const uploadedFiles = job.files.filter(
-    (/** @type {any} */ f) => f.status === 'completed' && f.upload_duration_seconds,
-  );
-  if (uploadedFiles.length > 0) {
-    const avgSeconds =
-      uploadedFiles.reduce(
-        (/** @type {number} */ sum, /** @type {any} */ f) => sum + f.upload_duration_seconds,
-        0,
-      ) / uploadedFiles.length;
-    setText('avg-file-time', formatDuration(avgSeconds));
+  // Single pass for average per-file duration (not pre-computed by backend)
+  let durationSum = 0;
+  let durationCount = 0;
+  for (const f of job.files) {
+    if (f.status === 'completed' && f.upload_duration_seconds) {
+      durationSum += f.upload_duration_seconds;
+      durationCount++;
+    }
+  }
+  setText('avg-file-time', durationCount > 0 ? formatDuration(durationSum / durationCount) : '-');
+
+  // Render first page and wire up pagination
+  renderCompletionPage();
+  wireCompletionPagination();
+
+  if (failed === 0) {
+    showNotification('Upload completed successfully!', 'success');
   } else {
-    setText('avg-file-time', '-');
+    showNotification(`Upload completed with ${failed} failed files`, 'error');
   }
+}
+
+/**
+ * Render the current page of the completion file table.
+ */
+function renderCompletionPage() {
+  if (!lastCompletedJob) return;
+
+  const files = lastCompletedJob.files;
+  const totalPages = Math.max(1, Math.ceil(files.length / COMPLETION_PAGE_SIZE));
+  const start = completionPage * COMPLETION_PAGE_SIZE;
+  const end = Math.min(start + COMPLETION_PAGE_SIZE, files.length);
+  const pageFiles = files.slice(start, end);
 
   const tbody = document.getElementById('completion-file-list');
   if (tbody) {
-    tbody.innerHTML = job.files
+    tbody.innerHTML = pageFiles
       .map((/** @type {any} */ file) => {
         let statusBadge;
         let statusClass;
@@ -109,10 +141,44 @@ export function showCompletionSummary(job) {
       .join('');
   }
 
-  if (failed === 0) {
-    showNotification('Upload completed successfully!', 'success');
-  } else {
-    showNotification(`Upload completed with ${failed} failed files`, 'error');
+  // Update pagination controls
+  setText('completion-page-info', `Page ${completionPage + 1} of ${totalPages}`);
+
+  const prevBtn = /** @type {HTMLButtonElement | null} */ (
+    document.getElementById('completion-prev-btn')
+  );
+  const nextBtn = /** @type {HTMLButtonElement | null} */ (
+    document.getElementById('completion-next-btn')
+  );
+  if (prevBtn) prevBtn.disabled = completionPage === 0;
+  if (nextBtn) nextBtn.disabled = completionPage >= totalPages - 1;
+}
+
+/**
+ * Wire up pagination button click handlers.
+ */
+function wireCompletionPagination() {
+  const prevBtn = document.getElementById('completion-prev-btn');
+  const nextBtn = document.getElementById('completion-next-btn');
+
+  if (prevBtn) {
+    prevBtn.onclick = () => {
+      if (completionPage > 0) {
+        completionPage--;
+        renderCompletionPage();
+      }
+    };
+  }
+
+  if (nextBtn) {
+    nextBtn.onclick = () => {
+      if (!lastCompletedJob) return;
+      const totalPages = Math.ceil(lastCompletedJob.files.length / COMPLETION_PAGE_SIZE);
+      if (completionPage < totalPages - 1) {
+        completionPage++;
+        renderCompletionPage();
+      }
+    };
   }
 }
 

From cc034bdafad6f3e20eab62dcd9b67dba85d286a1 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:59:00 -0700
Subject: [PATCH 011/173] JS: Add missing import

---
 app/static/js/modules/folder-browser.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/static/js/modules/folder-browser.js b/app/static/js/modules/folder-browser.js
index 663a0c1..a9e7292 100644
--- a/app/static/js/modules/folder-browser.js
+++ b/app/static/js/modules/folder-browser.js
@@ -1,4 +1,4 @@
-import { connectCombinedProgressStream } from './analysis.js';
+import { connectCombinedProgressStream, initStatusCounts } from './analysis.js';
 import { apiGet, apiPost } from './api.js';
 import { hideEl, setText, showEl } from './dom.js';
 import { formatBytes, formatMtime } from './formatters.js';

From 6be3766fee43c18fa29774cd18aeb66cf7838a77 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:59:23 -0700
Subject: [PATCH 012/173] Tests: Update completion summary test

---
 tests/js/upload-exec.test.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/js/upload-exec.test.js b/tests/js/upload-exec.test.js
index 4e34634..a1262d8 100644
--- a/tests/js/upload-exec.test.js
+++ b/tests/js/upload-exec.test.js
@@ -70,6 +70,9 @@ describe('upload-exec', () => {
                     { status: 'skipped', filename: 'c.mcap', file_size_formatted: '2 MB' },
                     { status: 'failed', filename: 'd.mcap', file_size_formatted: '1 MB' },
                 ],
+                files_uploaded: 2,
+                files_skipped: 1,
+                files_failed: 1,
                 successfully_uploaded_bytes_formatted: '8 MB',
                 total_upload_duration_formatted: '1m 30s',
                 average_upload_speed_mbps: 42.5,

From 7893d373617b7fedc9e72bee5f7c8d0aed438fd9 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 16 Feb 2026 13:59:44 -0700
Subject: [PATCH 013/173] Tests: Remove files from upload api test

---
 tests/test_routes.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_routes.py b/tests/test_routes.py
index cd4cb36..b73facd 100644
--- a/tests/test_routes.py
+++ b/tests/test_routes.py
@@ -138,7 +138,6 @@ def test_analyze_with_json_paths(self, client: FlaskClient) -> None:
 
         data = json.loads(response.data)
         assert "job_id" in data
-        assert "files" in data
         assert data["status"] == "analyzing"
 
     def test_get_status_not_found(self, client: FlaskClient) -> None:

From 5a91a55fa661fbbca2f08acf33229f2121b34aff Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:37:23 -0700
Subject: [PATCH 014/173] Cache: add info for uploaded files

---
 app/services/cache_service.py | 41 +++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/app/services/cache_service.py b/app/services/cache_service.py
index e925709..4a7dfcf 100644
--- a/app/services/cache_service.py
+++ b/app/services/cache_service.py
@@ -240,6 +240,47 @@ def bulk_update_cache(
 
         conn.commit()
 
+    def get_uploaded_file_info(
+        self,
+        bucket: str,
+        filename: str,
+        file_size: int,
+    ) -> dict[str, str | int] | None:
+        """Look up a cached upload entry by filename and size.
+
+        Returns the S3 path and file metadata for files where file_exists=1.
+        Used by the delete feature to cross-reference local files with S3 uploads.
+
+        Args:
+            bucket: S3 bucket name
+            filename: Original filename
+            file_size: File size in bytes
+
+        Returns:
+            Dict with s3_path, filename, file_size if found, else None
+        """
+        conn = self._get_connection()
+        cursor = conn.cursor()
+
+        cursor.execute(
+            """
+            SELECT s3_path, filename, file_size FROM s3_files
+            WHERE bucket = ? AND filename = ? AND file_size = ? AND file_exists = 1
+            LIMIT 1
+            """,
+            (bucket, filename, file_size),
+        )
+
+        row = cursor.fetchone()
+        if row is None:
+            return None
+
+        return {
+            "s3_path": row["s3_path"],
+            "filename": row["filename"],
+            "file_size": row["file_size"],
+        }
+
     def invalidate_bucket(self, bucket: str) -> int:
         """Invalidate all cache entries for a bucket.
 

From c6399f299252af31b57ea3de86b2cc4307f1b2d8 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:37:50 -0700
Subject: [PATCH 015/173] S3: Set multipart threshold upload to 1GB

Having smaller uploads means we can do hash checking against the
uploaded data without ETags or messing around which is a lot easier for
verification
---
 app/services/s3_service.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/app/services/s3_service.py b/app/services/s3_service.py
index f50740e..5b80a27 100644
--- a/app/services/s3_service.py
+++ b/app/services/s3_service.py
@@ -6,9 +6,27 @@
 from typing import Any
 
 import boto3
+from boto3.s3.transfer import TransferConfig
 from botocore.exceptions import ClientError, NoCredentialsError
 from mypy_boto3_s3 import S3Client
 
+# Multipart threshold: files below this size are uploaded as a single PUT request,
+# which produces a simple MD5 ETag. Files above use multipart upload, which produces
+# a composite ETag (md5_of_part_md5s-part_count) that can't be compared to a local MD5.
+#
+# The Local Delete feature relies on MD5 ETag comparison for integrity verification
+# before deleting local files. Lowering this threshold means more files get multipart
+# ETags and fall back to size-only verification (still safe, but less thorough).
+#
+# Guidelines:
+#   < 100 MB files  → single-part fine, no multipart benefit
+#   100 MB – 1 GB   → single-part fine on stable connections
+#   1 – 5 GB        → multipart recommended (retry resilience)
+#   > 5 GB          → multipart required (S3 hard limit)
+#
+# Our MCAP files are typically 50-100 MB, so 1 GB is very conservative.
+TRANSFER_CONFIG = TransferConfig(multipart_threshold=1024 * 1024 * 1024)  # 1 GB
+
 
 def get_available_profiles() -> list[str]:
     """Get list of available AWS profiles from ~/.aws/config and ~/.aws/credentials."""
@@ -122,6 +140,7 @@ def __call__(self, bytes_amount: int) -> None:
             Bucket=bucket,
             Key=key,
             Callback=progress,
+            Config=TRANSFER_CONFIG,
         )
 
         return {

From abbb2f96763c52d71b6a2c6d4f2ab5a742cf52e8 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:38:57 -0700
Subject: [PATCH 016/173] Upload: Add the ability to skip folders or files

---
 app/services/upload_manager.py | 30 ++++++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index 6cb3d6c..0057666 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -294,6 +294,8 @@ class ScanJob:
     total_already_uploaded: int = 0
     total_size: int = 0
     scanned_folders: list[dict[str, Any]] = field(default_factory=list)
+    excluded_subfolders: list[str] = field(default_factory=list)
+    excluded_files: list[str] = field(default_factory=list)
     created_at: datetime = field(default_factory=lambda: datetime.now(UTC))
     lock: threading.Lock = field(default_factory=threading.Lock, repr=False)
 
@@ -1150,17 +1152,29 @@ def check_s3(s3_path: str) -> bool:
         stats["file_statuses"] = file_statuses
         return files_to_analyze, stats
 
-    def create_scan_job(self, folder_path: str) -> ScanJob:
+    def create_scan_job(
+        self,
+        folder_path: str,
+        excluded_subfolders: list[str] | None = None,
+        excluded_files: list[str] | None = None,
+    ) -> ScanJob:
         """Create a new scan job for a folder.
 
         Args:
             folder_path: Root folder to scan
+            excluded_subfolders: Subfolder names to exclude from scan
+            excluded_files: Root-level filenames to exclude from scan
 
         Returns:
             The created ScanJob
         """
         job_id = str(uuid.uuid4())
-        scan_job = ScanJob(job_id=job_id, root_folder=folder_path)
+        scan_job = ScanJob(
+            job_id=job_id,
+            root_folder=folder_path,
+            excluded_subfolders=excluded_subfolders or [],
+            excluded_files=excluded_files or [],
+        )
         with self._lock:
             self.scan_jobs[job_id] = scan_job
         return scan_job
@@ -1211,12 +1225,24 @@ def scan_folder_async(
         log = get_log_service()
 
         try:
+            # Build exclusion sets for fast lookup
+            excluded_subs_set = set(scan_job.excluded_subfolders)
+            excluded_files_set = set(scan_job.excluded_files)
+
             # Phase 1: Enumerate subfolders containing .mcap files (fast, metadata only)
             folder_map: dict[str, list[Path]] = {}
             for mcap_path in root.rglob("*.mcap"):
                 if scan_job.cancelled:
                     break
                 if mcap_path.is_file():
+                    rel = mcap_path.relative_to(root)
+                    parts = rel.parts
+                    # Skip root-level files in excluded_files list
+                    if len(parts) == 1 and parts[0] in excluded_files_set:
+                        continue
+                    # Skip files under excluded subfolders
+                    if len(parts) > 1 and parts[0] in excluded_subs_set:
+                        continue
                     parent = str(mcap_path.parent)
                     if parent not in folder_map:
                         folder_map[parent] = []

From 8a78d68de4516639945ce8b411307db59e1a31d3 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:39:24 -0700
Subject: [PATCH 017/173] Logs: Add more details about csv data

---
 app/services/log_service.py | 128 +++++++++++++++++++++++++++++++++++-
 1 file changed, 125 insertions(+), 3 deletions(-)

diff --git a/app/services/log_service.py b/app/services/log_service.py
index 2d06715..ba2a4d6 100644
--- a/app/services/log_service.py
+++ b/app/services/log_service.py
@@ -417,8 +417,18 @@ def get_log_stats(self) -> dict[str, Any]:
 
         dates.sort()
 
-        # Count CSV files
-        csv_count = len(list(csv_dir.rglob("*.csv"))) if csv_dir.exists() else 0
+        # Collect CSV file details
+        csv_files: list[dict[str, Any]] = []
+        if csv_dir.exists():
+            for csv_file in sorted(csv_dir.rglob("*.csv"), reverse=True):
+                date_str = self._extract_date_from_hive_path(csv_file) or ""
+                rel_path = str(csv_file.relative_to(log_dir))
+                csv_files.append({
+                    "path": rel_path,
+                    "filename": csv_file.name,
+                    "date": date_str,
+                    "size": csv_file.stat().st_size,
+                })
 
         return {
             "total_entries": total_entries,
@@ -431,7 +441,119 @@ def get_log_stats(self) -> dict[str, Any]:
                 "latest": dates[-1] if dates else None,
             },
             "file_count": len(event_files),
-            "csv_count": csv_count,
+            "csv_count": len(csv_files),
+            "csv_files": csv_files,
+        }
+
+    def get_upload_stats(self) -> dict[str, Any]:
+        """Parse all CSV upload summary files and return aggregated stats.
+
+        Returns:
+            Dict with global totals and per-session detail including file rows.
+        """
+        from app.services.utils import format_file_size
+
+        log_dir = self._get_log_dir()
+        csv_dir = log_dir / "csv"
+
+        total_uploaded = 0
+        total_failed = 0
+        total_skipped = 0
+        total_bytes = 0
+        sessions: list[dict[str, Any]] = []
+
+        if not csv_dir.exists():
+            return {
+                "total_files_uploaded": 0,
+                "total_files_failed": 0,
+                "total_files_skipped": 0,
+                "total_bytes_uploaded": 0,
+                "total_sessions": 0,
+                "sessions": [],
+            }
+
+        for csv_file in sorted(csv_dir.rglob("*.csv"), reverse=True):
+            rel_path = str(csv_file.relative_to(log_dir))
+            date_str = self._extract_date_from_hive_path(csv_file) or ""
+
+            # Extract time from filename: upload-summary-HHMMSS-shortid.csv
+            fname = csv_file.stem  # e.g. upload-summary-143022-abcd1234
+            parts = fname.split("-")
+            time_str = ""
+            if len(parts) >= 3:
+                raw_time = parts[2]  # "143022"
+                if len(raw_time) == 6 and raw_time.isdigit():
+                    time_str = f"{raw_time[:2]}:{raw_time[2:4]}:{raw_time[4:6]}"
+
+            session_files: list[dict[str, Any]] = []
+            session_completed = 0
+            session_failed = 0
+            session_skipped = 0
+            session_bytes = 0
+            session_duration = 0.0
+
+            try:
+                with open(csv_file, encoding="utf-8", newline="") as fh:
+                    reader = csv.DictReader(fh)
+                    for row in reader:
+                        status = row.get("status", "")
+                        size_bytes = int(row.get("file_size_bytes", "0") or "0")
+                        duration = float(row.get("upload_duration_seconds", "0") or "0")
+                        speed = row.get("upload_speed_mbps", "")
+
+                        if status == "completed":
+                            session_completed += 1
+                            session_bytes += size_bytes
+                        elif status == "failed":
+                            session_failed += 1
+                        elif status == "skipped":
+                            session_skipped += 1
+
+                        session_duration += duration
+
+                        session_files.append({
+                            "filename": row.get("filename", ""),
+                            "file_size_formatted": row.get("file_size_formatted", ""),
+                            "status": status,
+                            "upload_speed_mbps": speed,
+                            "s3_path": row.get("s3_path", ""),
+                            "error_message": row.get("error_message", ""),
+                        })
+            except (OSError, csv.Error):
+                continue
+
+            total_uploaded += session_completed
+            total_failed += session_failed
+            total_skipped += session_skipped
+            total_bytes += session_bytes
+
+            avg_speed = 0.0
+            if session_duration > 0 and session_bytes > 0:
+                avg_speed = round(session_bytes / session_duration / 1024 / 1024 * 8, 1)
+
+            sessions.append({
+                "csv_path": rel_path,
+                "date": date_str,
+                "time": time_str,
+                "total_files": len(session_files),
+                "completed": session_completed,
+                "failed": session_failed,
+                "skipped": session_skipped,
+                "total_bytes": session_bytes,
+                "total_bytes_formatted": format_file_size(session_bytes),
+                "total_duration_seconds": round(session_duration, 1),
+                "avg_speed_mbps": avg_speed,
+                "files": session_files,
+            })
+
+        return {
+            "total_files_uploaded": total_uploaded,
+            "total_files_failed": total_failed,
+            "total_files_skipped": total_skipped,
+            "total_bytes_uploaded": total_bytes,
+            "total_bytes_uploaded_formatted": format_file_size(total_bytes),
+            "total_sessions": len(sessions),
+            "sessions": sessions,
         }
 
     def sync_logs_to_s3(

From 35530cea91568059be6bc52a4defd0e3472dc15d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:39:45 -0700
Subject: [PATCH 018/173] Route: Add exclusions to upload

---
 app/routes/upload.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/app/routes/upload.py b/app/routes/upload.py
index b6e76e0..f736be9 100644
--- a/app/routes/upload.py
+++ b/app/routes/upload.py
@@ -455,11 +455,17 @@ def scan_folder_async() -> tuple[Response, int]:
         return jsonify({"error": f"Path is not a directory: {folder_path}"}), 400
 
     cache_only: bool = data.get("cache_only", False)
+    excluded_subfolders: list[str] = data.get("excluded_subfolders", [])
+    excluded_files: list[str] = data.get("excluded_files", [])
 
     settings = get_settings()
     manager = get_upload_manager()
 
-    scan_job = manager.create_scan_job(str(folder_path.absolute()))
+    scan_job = manager.create_scan_job(
+        str(folder_path.absolute()),
+        excluded_subfolders=excluded_subfolders,
+        excluded_files=excluded_files,
+    )
 
     def scan_progress_callback(job_id: str, event_data: dict[str, Any]) -> None:
         send_sse_event(job_id, event_data)

From 65ac82951bad6f324f5bdca43f95b96254529783 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:40:12 -0700
Subject: [PATCH 019/173] Settings: Add overall success message

---
 app/routes/settings.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/app/routes/settings.py b/app/routes/settings.py
index bc1e1a6..486f72c 100644
--- a/app/routes/settings.py
+++ b/app/routes/settings.py
@@ -192,10 +192,7 @@ def run_update() -> tuple[Response, int]:
     result = updater.update_application()
 
     # Determine overall success
-    all_success = all(
-        step["success"]
-        for step in [result["git_pull"], result["pip_install"], result["modaq_toolkit"]]
-    )
+    all_success = all(step["success"] for step in result.values())
 
     return jsonify(
         {

From 26a97a1fc89c60212107db240fe10647d7787c12 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:40:50 -0700
Subject: [PATCH 020/173] File Manager: Add/leverage caching

---
 app/routes/files.py | 98 +++++++++++++++++++++++++++++++--------------
 1 file changed, 68 insertions(+), 30 deletions(-)

diff --git a/app/routes/files.py b/app/routes/files.py
index 3b122e0..fb19351 100644
--- a/app/routes/files.py
+++ b/app/routes/files.py
@@ -6,6 +6,7 @@
 
 from app.config import get_settings
 from app.services import s3_service
+from app.services.cache_service import get_cache_service
 
 files_bp = Blueprint("files", __name__)
 
@@ -163,12 +164,16 @@ def browse_local() -> tuple[Response, int]:
     Returns:
         JSON response with folders, files, and navigation info
     """
-    # Get requested path, default to home directory
+    # Get requested path, default to configured upload folder or home directory
     requested_path = request.args.get("path", "")
 
     if not requested_path:
-        # Default to home directory
-        requested_path = str(Path.home())
+        settings = get_settings()
+        default_folder = settings.default_upload_folder
+        if default_folder and Path(default_folder).is_dir():
+            requested_path = default_folder
+        else:
+            requested_path = str(Path.home())
 
     path = Path(requested_path)
 
@@ -189,51 +194,82 @@ def browse_local() -> tuple[Response, int]:
     if not path.is_dir():
         return jsonify({"error": f"Not a directory: {path}"}), 400
 
-    # Build response
-    folders: list[dict[str, str | int]] = []
-    files: list[dict[str, str | int | float]] = []
+    # Build response — single-pass rglob for recursive MCAP counts + cache checks
+    cache = get_cache_service()
+    bucket = g.settings.s3_bucket
+
+    folder_mcap_counts: dict[str, int] = {}
+    folder_uploaded_counts: dict[str, int] = {}
+    files: list[dict[str, str | int | float | bool]] = []
     mcap_count = 0
+    direct_uploaded = 0
 
     try:
-        for entry in sorted(path.iterdir(), key=lambda x: (not x.is_dir(), x.name.lower())):
-            # Skip hidden files/folders (starting with .)
-            if entry.name.startswith("."):
+        for mcap_path in path.rglob("*.mcap"):
+            # Skip hidden paths (any component starting with .)
+            if any(part.startswith(".") for part in mcap_path.relative_to(path).parts):
                 continue
 
+            # Check cache for already-uploaded status
             try:
-                if entry.is_dir():
-                    # Count MCAP files in this folder (non-recursive, for preview)
-                    try:
-                        mcap_in_folder = sum(1 for f in entry.iterdir() if f.suffix == ".mcap")
-                    except PermissionError:
-                        mcap_in_folder = 0
+                file_stat = mcap_path.stat()
+                uploaded = cache.check_exists_by_filename(
+                    bucket, mcap_path.name, file_stat.st_size
+                ) is True
+            except PermissionError:
+                continue
+
+            rel = mcap_path.relative_to(path)
+            parts = rel.parts
+            if len(parts) == 1:
+                # Direct child MCAP file
+                mcap_count += 1
+                if uploaded:
+                    direct_uploaded += 1
+                files.append(
+                    {
+                        "name": mcap_path.name,
+                        "path": str(mcap_path),
+                        "size": file_stat.st_size,
+                        "mtime": file_stat.st_mtime,
+                        "already_uploaded": uploaded,
+                    }
+                )
+            else:
+                # Nested — attribute to the immediate subfolder
+                folder_name = parts[0]
+                folder_mcap_counts[folder_name] = folder_mcap_counts.get(folder_name, 0) + 1
+                if uploaded:
+                    folder_uploaded_counts[folder_name] = (
+                        folder_uploaded_counts.get(folder_name, 0) + 1
+                    )
+    except PermissionError:
+        return jsonify({"error": f"Permission denied: {path}"}), 403
 
+    # Build folder list from direct children (non-hidden directories)
+    folders: list[dict[str, str | int]] = []
+    try:
+        for entry in sorted(path.iterdir(), key=lambda x: x.name.lower()):
+            if entry.name.startswith("."):
+                continue
+            try:
+                if entry.is_dir():
                     folders.append(
                         {
                             "name": entry.name,
                             "path": str(entry),
-                            "mcap_count": mcap_in_folder,
+                            "mcap_count": folder_mcap_counts.get(entry.name, 0),
+                            "already_uploaded": folder_uploaded_counts.get(entry.name, 0),
                         }
                     )
-                elif entry.is_file():
-                    if entry.suffix == ".mcap":
-                        mcap_count += 1
-                        file_stat = entry.stat()
-                        files.append(
-                            {
-                                "name": entry.name,
-                                "path": str(entry),
-                                "size": file_stat.st_size,
-                                "mtime": file_stat.st_mtime,
-                            }
-                        )
             except PermissionError:
-                # Skip entries we can't access
                 continue
-
     except PermissionError:
         return jsonify({"error": f"Permission denied: {path}"}), 403
 
+    # Sort files by name
+    files.sort(key=lambda f: str(f["name"]).lower())
+
     # Build breadcrumbs for navigation
     breadcrumbs: list[dict[str, str]] = []
     current = path
@@ -269,5 +305,7 @@ def browse_local() -> tuple[Response, int]:
             "folders": folders,
             "files": files,  # Only MCAP files
             "mcap_count": mcap_count,
+            "total_mcap_count": mcap_count + sum(folder_mcap_counts.values()),
+            "already_uploaded": direct_uploaded + sum(folder_uploaded_counts.values()),
         }
     ), 200

From 3a1449a5c76c9e63ec606cd55fceef91e3b9b484 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:41:12 -0700
Subject: [PATCH 021/173] Route: Add logs upload stats

---
 app/routes/logs.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/app/routes/logs.py b/app/routes/logs.py
index 6017f08..394783f 100644
--- a/app/routes/logs.py
+++ b/app/routes/logs.py
@@ -79,6 +79,18 @@ def get_log_stats() -> tuple[Response, int]:
     return jsonify(stats), 200
 
 
+@logs_bp.route("/upload-stats", methods=["GET"])
+def get_upload_stats() -> tuple[Response, int]:
+    """Get aggregated upload statistics from CSV summaries.
+
+    Returns:
+        JSON with global totals and per-session detail including file rows.
+    """
+    log = get_log_service()
+    stats = log.get_upload_stats()
+    return jsonify(stats), 200
+
+
 @logs_bp.route("/sync", methods=["POST"])
 def sync_logs() -> tuple[Response, int]:
     """Trigger S3 sync of log files.

From 93a74a6ff45277781c45c9ae6dfd51443e84c08a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:41:51 -0700
Subject: [PATCH 022/173] Tests: Update routes for reactjs changes

---
 tests/test_routes.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/test_routes.py b/tests/test_routes.py
index b73facd..9c9b1c8 100644
--- a/tests/test_routes.py
+++ b/tests/test_routes.py
@@ -10,22 +10,22 @@ class TestMainRoutes:
     """Tests for main page routes."""
 
     def test_index_page(self, client: FlaskClient) -> None:
-        """Test that index page loads successfully."""
+        """Test that index page serves the React SPA shell."""
         response = client.get("/")
         assert response.status_code == 200
-        assert b"Upload MCAP Files" in response.data
+        assert b'<div id="root">' in response.data
 
     def test_files_page(self, client: FlaskClient) -> None:
-        """Test that files page loads successfully."""
+        """Test that files page serves the React SPA shell."""
         response = client.get("/files")
         assert response.status_code == 200
-        assert b"S3 File Browser" in response.data
+        assert b'<div id="root">' in response.data
 
     def test_settings_page(self, client: FlaskClient) -> None:
-        """Test that settings page loads successfully."""
+        """Test that settings page serves the React SPA shell."""
         response = client.get("/settings")
         assert response.status_code == 200
-        assert b"Settings" in response.data
+        assert b'<div id="root">' in response.data
 
 
 class TestSettingsAPI:
@@ -252,10 +252,10 @@ class TestLogsAPI:
     """Tests for logs API endpoints."""
 
     def test_logs_page(self, client: FlaskClient) -> None:
-        """Test that logs page loads successfully."""
+        """Test that logs page serves the React SPA shell."""
         response = client.get("/logs")
         assert response.status_code == 200
-        assert b"Application Logs" in response.data
+        assert b'<div id="root">' in response.data
 
     def test_get_entries(self, client: FlaskClient) -> None:
         """Test getting log entries."""

From bd84e27374359ea34e290e98538e53155ea8a324 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:42:13 -0700
Subject: [PATCH 023/173] Routes: Refactor main for React SPA

---
 app/routes/main.py | 43 +++++++++++++++++++++++++------------------
 1 file changed, 25 insertions(+), 18 deletions(-)

diff --git a/app/routes/main.py b/app/routes/main.py
index 700e234..76107ba 100644
--- a/app/routes/main.py
+++ b/app/routes/main.py
@@ -1,29 +1,36 @@
-"""Main page routes for modaq_upload"""
+"""Main page routes for modaq_upload — serves the React SPA."""
 
-from flask import Blueprint, render_template
+import os
 
-main_bp = Blueprint("main", __name__)
+from flask import Blueprint, Response, send_from_directory
 
+main_bp = Blueprint("main", __name__)
 
-@main_bp.route("/")
-def index() -> str:
-    """Render the upload page."""
-    return render_template("index.html")
+# Path to the React production build
+FRONTEND_DIST = os.path.join(
+    os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))),
+    "frontend",
+    "dist",
+)
 
 
+@main_bp.route("/")
+@main_bp.route("/delete")
 @main_bp.route("/files")
-def files() -> str:
-    """Render the S3 file browser page."""
-    return render_template("files.html")
+@main_bp.route("/settings")
+@main_bp.route("/logs")
+def serve_spa() -> Response:
+    """Serve React's index.html for all client-side routes."""
+    return send_from_directory(FRONTEND_DIST, "index.html")
 
 
-@main_bp.route("/settings")
-def settings() -> str:
-    """Render the settings page."""
-    return render_template("settings.html")
+@main_bp.route("/assets/<path:filename>")
+def serve_assets(filename: str) -> Response:
+    """Serve Vite-built static assets (JS, CSS)."""
+    return send_from_directory(os.path.join(FRONTEND_DIST, "assets"), filename)
 
 
-@main_bp.route("/logs")
-def logs() -> str:
-    """Render the logs viewer page."""
-    return render_template("logs.html")
+@main_bp.route("/images/<path:filename>")
+def serve_images(filename: str) -> Response:
+    """Serve image assets from the public directory."""
+    return send_from_directory(os.path.join(FRONTEND_DIST, "images"), filename)

From 78138ad6beed7afaa9eaedc66101feddb64cbafc Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:42:43 -0700
Subject: [PATCH 024/173] Config: Rebuild npm on update

---
 app/config.py | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/app/config.py b/app/config.py
index 432314c..4f78506 100644
--- a/app/config.py
+++ b/app/config.py
@@ -241,11 +241,19 @@ def update_application(self) -> dict[str, Any]:
             "git_pull": {"success": False, "output": ""},
             "pip_install": {"success": False, "output": ""},
             "modaq_toolkit": {"success": False, "output": ""},
+            "npm_install": {"success": False, "output": ""},
+            "frontend_build": {"success": False, "output": ""},
         }
 
-        steps: list[tuple[str, list[str]]] = [
-            ("git_pull", ["git", "pull"]),
-            ("pip_install", [sys.executable, "-m", "pip", "install", "-r", "requirements.txt"]),
+        frontend_dir = str(self.base_dir / "frontend")
+
+        steps: list[tuple[str, list[str], str | None]] = [
+            ("git_pull", ["git", "pull"], None),
+            (
+                "pip_install",
+                [sys.executable, "-m", "pip", "install", "-r", "requirements.txt"],
+                None,
+            ),
             (
                 "modaq_toolkit",
                 [
@@ -257,14 +265,17 @@ def update_application(self) -> dict[str, Any]:
                     "--force-reinstall",
                     "git+https://github.com/MODAQ2/MODAQ_toolkit.git",
                 ],
+                None,
             ),
+            ("npm_install", ["npm", "install"], frontend_dir),
+            ("frontend_build", ["npm", "run", "build"], frontend_dir),
         ]
 
-        for step_name, cmd in steps:
+        for step_name, cmd, cwd in steps:
             try:
                 result = subprocess.run(
                     cmd,
-                    cwd=self.base_dir,
+                    cwd=cwd or self.base_dir,
                     capture_output=True,
                     text=True,
                     check=True,

From 5ffa127673489dfc67164750f96ed0eb494160e0 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:43:00 -0700
Subject: [PATCH 025/173] App: Add delete api route

---
 app/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/app/__init__.py b/app/__init__.py
index 7c69fc9..aaa06e4 100644
--- a/app/__init__.py
+++ b/app/__init__.py
@@ -25,6 +25,7 @@ def inject_display_name() -> dict[str, str]:
         return {"display_name": settings.display_name}
 
     # Register blueprints
+    from app.routes.delete import delete_bp
     from app.routes.files import files_bp
     from app.routes.logs import logs_bp
     from app.routes.main import main_bp
@@ -36,6 +37,7 @@ def inject_display_name() -> dict[str, str]:
     app.register_blueprint(files_bp, url_prefix="/api/files")
     app.register_blueprint(settings_bp, url_prefix="/api/settings")
     app.register_blueprint(logs_bp, url_prefix="/api/logs")
+    app.register_blueprint(delete_bp, url_prefix="/api/delete")
 
     # Log application startup
     from app.services.log_service import get_log_service

From bc741ed2a0f84f8b91074a94e52abb588d424c0c Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:43:26 -0700
Subject: [PATCH 026/173] App: Add delete route

---
 app/routes/delete.py | 223 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 223 insertions(+)
 create mode 100644 app/routes/delete.py

diff --git a/app/routes/delete.py b/app/routes/delete.py
new file mode 100644
index 0000000..2f34db7
--- /dev/null
+++ b/app/routes/delete.py
@@ -0,0 +1,223 @@
+"""Delete API routes for local file cleanup after S3 upload."""
+
+import json
+import threading
+import time
+from collections import deque
+from collections.abc import Generator
+from pathlib import Path
+from typing import Any
+
+from flask import Blueprint, Response, jsonify, request
+
+from app.config import get_settings
+from app.services.delete_manager import DeleteJob, get_delete_manager
+
+delete_bp = Blueprint("delete", __name__)
+
+# SSE client queues for delete jobs
+_sse_queues: dict[str, list[deque[dict[str, Any]]]] = {}
+_sse_lock = threading.Lock()
+
+
+def _send_sse_event(job_id: str, data: dict[str, Any]) -> None:
+    """Send an SSE event to all clients listening for a delete job."""
+    with _sse_lock:
+        queues = _sse_queues.get(job_id, [])
+        for q in queues:
+            q.append(data)
+
+
+@delete_bp.route("/scan", methods=["POST"])
+def scan_folder() -> tuple[Response, int]:
+    """Scan a folder for deletable MCAP files.
+
+    Cross-references local .mcap files with the upload cache to find
+    files that have been uploaded to S3.
+
+    Request body:
+        folder_path: Path to scan for MCAP files
+
+    Returns:
+        JSON with job_id, matched files, and stats
+    """
+    if not request.is_json:
+        return jsonify({"error": "JSON body required"}), 400
+
+    data = request.get_json()
+    if not data or "folder_path" not in data:
+        return jsonify({"error": "folder_path is required"}), 400
+
+    folder_path = Path(data["folder_path"])
+
+    if not folder_path.exists():
+        return jsonify({"error": f"Folder not found: {folder_path}"}), 404
+
+    if not folder_path.is_dir():
+        return jsonify({"error": f"Path is not a directory: {folder_path}"}), 400
+
+    settings = get_settings()
+    manager = get_delete_manager()
+
+    try:
+        job = manager.scan_folder(str(folder_path.absolute()), settings.s3_bucket)
+    except PermissionError as e:
+        return jsonify({"error": f"Permission denied: {e}"}), 403
+
+    total_size = sum(f.file_size for f in job.files)
+
+    return jsonify({
+        "success": True,
+        "job_id": job.job_id,
+        "folder_path": str(folder_path.absolute()),
+        "files": [f.to_dict() for f in job.files],
+        "total_files": len(job.files),
+        "total_size": total_size,
+    }), 200
+
+
+@delete_bp.route("/start/<job_id>", methods=["POST"])
+def start_delete(job_id: str) -> tuple[Response, int]:
+    """Start verification and deletion for a delete job.
+
+    Args:
+        job_id: The delete job to start
+
+    Returns:
+        JSON with job status
+    """
+    settings = get_settings()
+    manager = get_delete_manager()
+
+    job = manager.get_job(job_id)
+    if not job:
+        return jsonify({"error": "Job not found"}), 404
+
+    def progress_callback(job: DeleteJob) -> None:
+        """Send progress updates via SSE."""
+        if job.status in ("completed", "failed", "cancelled"):
+            _send_sse_event(job.job_id, {"type": "delete_complete", **job.to_dict()})
+        else:
+            _send_sse_event(
+                job.job_id, {"type": "delete_progress", **job.to_progress_dict()}
+            )
+
+    def run_delete() -> None:
+        manager.start_delete_job(
+            job_id,
+            settings.aws_profile,
+            settings.aws_region,
+            progress_callback=progress_callback,
+        )
+
+    thread = threading.Thread(target=run_delete, daemon=True)
+    thread.start()
+
+    return jsonify({"job_id": job_id, "status": "started"}), 200
+
+
+@delete_bp.route("/progress/<job_id>", methods=["GET"])
+def get_progress(job_id: str) -> Response:
+    """Stream progress updates for a delete job via SSE.
+
+    Args:
+        job_id: The delete job to monitor
+
+    Returns:
+        SSE stream of progress updates
+    """
+    manager = get_delete_manager()
+
+    def generate() -> Generator[str, None, None]:
+        queue: deque[dict[str, Any]] = deque()
+        with _sse_lock:
+            if job_id not in _sse_queues:
+                _sse_queues[job_id] = []
+            _sse_queues[job_id].append(queue)
+
+        try:
+            # Send initial state
+            job = manager.get_job(job_id)
+            if job:
+                yield f"data: {json.dumps(job.to_progress_dict())}\n\n"
+
+            while True:
+                while queue:
+                    data = queue.popleft()
+                    yield f"data: {json.dumps(data)}\n\n"
+
+                    # Terminal events
+                    if data.get("type") == "delete_complete":
+                        return
+
+                time.sleep(0.1)
+
+                # Check if job still exists
+                job = manager.get_job(job_id)
+                if not job:
+                    yield 'data: {"error": "Job not found"}\n\n'
+                    return
+
+                # Handle race: job completed before client connected
+                if job.status in ("completed", "failed", "cancelled"):
+                    yield f"data: {json.dumps({'type': 'delete_complete', **job.to_dict()})}\n\n"
+                    return
+
+        finally:
+            with _sse_lock:
+                if job_id in _sse_queues and queue in _sse_queues[job_id]:
+                    _sse_queues[job_id].remove(queue)
+                    if not _sse_queues[job_id]:
+                        del _sse_queues[job_id]
+
+    return Response(
+        generate(),
+        mimetype="text/event-stream",
+        headers={
+            "Cache-Control": "no-cache",
+            "Connection": "keep-alive",
+            "X-Accel-Buffering": "no",
+        },
+    )
+
+
+@delete_bp.route("/status/<job_id>", methods=["GET"])
+def get_status(job_id: str) -> tuple[Response, int]:
+    """Get current status of a delete job (non-streaming).
+
+    Args:
+        job_id: The delete job to check
+
+    Returns:
+        JSON with job status
+    """
+    manager = get_delete_manager()
+
+    job = manager.get_job(job_id)
+    if not job:
+        return jsonify({"error": "Job not found"}), 404
+
+    return jsonify(job.to_dict()), 200
+
+
+@delete_bp.route("/cancel/<job_id>", methods=["POST"])
+def cancel_delete(job_id: str) -> tuple[Response, int]:
+    """Cancel a delete job.
+
+    Args:
+        job_id: The delete job to cancel
+
+    Returns:
+        JSON with cancellation status
+    """
+    manager = get_delete_manager()
+
+    if manager.cancel_job(job_id):
+        job = manager.get_job(job_id)
+        return jsonify({
+            "success": True,
+            "job_id": job_id,
+            "job": job.to_dict() if job else None,
+        }), 200
+
+    return jsonify({"error": "Job not found"}), 404

From d88eab1ba57461a63b0b24d1ff2de7656b82528e Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:43:38 -0700
Subject: [PATCH 027/173] Service: Add delete manager service

---
 app/services/delete_manager.py | 487 +++++++++++++++++++++++++++++++++
 1 file changed, 487 insertions(+)
 create mode 100644 app/services/delete_manager.py

diff --git a/app/services/delete_manager.py b/app/services/delete_manager.py
new file mode 100644
index 0000000..671909e
--- /dev/null
+++ b/app/services/delete_manager.py
@@ -0,0 +1,487 @@
+"""Delete manager service for local file cleanup after S3 upload."""
+
+import hashlib
+import os
+import threading
+import uuid
+from collections.abc import Callable
+from concurrent.futures import ThreadPoolExecutor
+from dataclasses import dataclass, field
+from datetime import UTC, datetime
+from enum import Enum
+from pathlib import Path
+from typing import Any
+
+from app.services.cache_service import get_cache_service
+from app.services.log_service import get_log_service
+from app.services.s3_service import create_s3_client, get_object_metadata
+
+
+class DeleteStatus(Enum):
+    """Status for individual files in a delete job."""
+
+    PENDING = "pending"
+    SCANNING = "scanning"
+    VERIFYING = "verifying"
+    VERIFIED = "verified"
+    DELETING = "deleting"
+    DELETED = "deleted"
+    MISMATCH = "mismatch"
+    FAILED = "failed"
+    CANCELLED = "cancelled"
+
+
+@dataclass
+class FileDeleteState:
+    """State for a single file in a delete job."""
+
+    filename: str
+    local_path: str
+    file_size: int
+    s3_path: str
+    s3_bucket: str
+    status: DeleteStatus = DeleteStatus.PENDING
+    local_md5: str = ""
+    s3_etag: str = ""
+    s3_size: int = 0
+    verification: str = ""
+    error_message: str = ""
+
+    def to_dict(self) -> dict[str, Any]:
+        """Serialize to dictionary for API responses."""
+        return {
+            "filename": self.filename,
+            "local_path": self.local_path,
+            "file_size": self.file_size,
+            "s3_path": self.s3_path,
+            "s3_bucket": self.s3_bucket,
+            "status": self.status.value,
+            "local_md5": self.local_md5,
+            "s3_etag": self.s3_etag,
+            "s3_size": self.s3_size,
+            "verification": self.verification,
+            "error_message": self.error_message,
+        }
+
+
+@dataclass
+class DeleteJob:
+    """A delete job tracking multiple files."""
+
+    job_id: str
+    files: list[FileDeleteState] = field(default_factory=list)
+    status: str = "pending"
+    created_at: str = field(default_factory=lambda: datetime.now(UTC).isoformat())
+    started_at: str | None = None
+    completed_at: str | None = None
+    cancelled: bool = False
+    lock: threading.Lock = field(default_factory=threading.Lock)
+
+    def to_dict(self) -> dict[str, Any]:
+        """Serialize to dictionary for API responses."""
+        with self.lock:
+            status_counts: dict[str, int] = {}
+            total_deleted_size = 0
+            for f in self.files:
+                status_counts[f.status.value] = status_counts.get(f.status.value, 0) + 1
+                if f.status == DeleteStatus.DELETED:
+                    total_deleted_size += f.file_size
+
+            return {
+                "job_id": self.job_id,
+                "status": self.status,
+                "total_files": len(self.files),
+                "files": [f.to_dict() for f in self.files],
+                "status_counts": status_counts,
+                "total_deleted_size": total_deleted_size,
+                "created_at": self.created_at,
+                "started_at": self.started_at,
+                "completed_at": self.completed_at,
+                "cancelled": self.cancelled,
+            }
+
+    def to_progress_dict(self) -> dict[str, Any]:
+        """Lightweight progress for SSE streaming."""
+        with self.lock:
+            status_counts: dict[str, int] = {}
+            total_deleted_size = 0
+            for f in self.files:
+                status_counts[f.status.value] = status_counts.get(f.status.value, 0) + 1
+                if f.status == DeleteStatus.DELETED:
+                    total_deleted_size += f.file_size
+
+            files_processed = sum(
+                1
+                for f in self.files
+                if f.status
+                not in (DeleteStatus.PENDING, DeleteStatus.VERIFYING, DeleteStatus.DELETING)
+            )
+
+            return {
+                "job_id": self.job_id,
+                "status": self.status,
+                "total_files": len(self.files),
+                "files_processed": files_processed,
+                "status_counts": status_counts,
+                "total_deleted_size": total_deleted_size,
+                "cancelled": self.cancelled,
+            }
+
+
+def compute_md5(file_path: str, chunk_size: int = 8 * 1024 * 1024) -> str:
+    """Compute MD5 hash of a file in chunks.
+
+    Args:
+        file_path: Path to the file
+        chunk_size: Read chunk size in bytes (default 8MB)
+
+    Returns:
+        Hex-encoded MD5 hash string
+    """
+    md5 = hashlib.md5()  # noqa: S324
+    with open(file_path, "rb") as f:
+        while True:
+            chunk = f.read(chunk_size)
+            if not chunk:
+                break
+            md5.update(chunk)
+    return md5.hexdigest()
+
+
+def is_multipart_etag(etag: str) -> bool:
+    """Check if an S3 ETag indicates a multipart upload.
+
+    Multipart ETags contain a hyphen followed by the number of parts.
+
+    Args:
+        etag: S3 ETag string (already stripped of quotes)
+
+    Returns:
+        True if this is a multipart ETag
+    """
+    return "-" in etag
+
+
+class DeleteManager:
+    """Manages local file deletion jobs with MD5 verification against S3."""
+
+    def __init__(self) -> None:
+        self.jobs: dict[str, DeleteJob] = {}
+
+    def scan_folder(self, folder_path: str, bucket: str) -> DeleteJob:
+        """Scan a folder for .mcap files and cross-reference with upload cache.
+
+        Args:
+            folder_path: Local directory to scan
+            bucket: S3 bucket to check against
+
+        Returns:
+            A new DeleteJob with files matched against the cache
+        """
+        job_id = str(uuid.uuid4())
+        job = DeleteJob(job_id=job_id)
+        cache = get_cache_service()
+        folder = Path(folder_path)
+
+        for mcap_path in sorted(folder.rglob("*.mcap")):
+            if not mcap_path.is_file():
+                continue
+
+            stat = mcap_path.stat()
+            file_size = stat.st_size
+            filename = mcap_path.name
+
+            # Look up in cache
+            cache_info = cache.get_uploaded_file_info(bucket, filename, file_size)
+
+            if cache_info is not None:
+                file_state = FileDeleteState(
+                    filename=filename,
+                    local_path=str(mcap_path.absolute()),
+                    file_size=file_size,
+                    s3_path=str(cache_info["s3_path"]),
+                    s3_bucket=bucket,
+                )
+                job.files.append(file_state)
+
+        self.jobs[job_id] = job
+        return job
+
+    def start_delete_job(
+        self,
+        job_id: str,
+        aws_profile: str,
+        aws_region: str,
+        progress_callback: Callable[[DeleteJob], None] | None = None,
+    ) -> bool:
+        """Start verification and deletion for a job.
+
+        Phase 1: Compute local MD5 hashes (parallel)
+        Phase 2: Verify against S3 via HEAD — size match (primary) + MD5 (secondary)
+        Phase 3: Delete verified files (sequential)
+
+        Args:
+            job_id: The job to start
+            aws_profile: AWS profile name
+            aws_region: AWS region
+            progress_callback: Called after each file status change
+
+        Returns:
+            True if job was started
+        """
+        job = self.jobs.get(job_id)
+        if not job:
+            return False
+
+        with job.lock:
+            job.status = "verifying"
+            job.started_at = datetime.now(UTC).isoformat()
+
+        log = get_log_service()
+        log.info(
+            "delete",
+            "job_started",
+            f"Delete job started: {len(job.files)} files",
+            {"job_id": job_id, "total_files": len(job.files)},
+        )
+
+        # Phase 1: Compute local MD5 hashes
+        def compute_file_md5(file_state: FileDeleteState) -> None:
+            if job.cancelled:
+                return
+            with job.lock:
+                file_state.status = DeleteStatus.VERIFYING
+            if progress_callback:
+                progress_callback(job)
+
+            try:
+                file_state.local_md5 = compute_md5(file_state.local_path)
+            except Exception as e:
+                with job.lock:
+                    file_state.status = DeleteStatus.FAILED
+                    file_state.error_message = f"MD5 computation failed: {e}"
+                log.error(
+                    "delete",
+                    "md5_failed",
+                    f"MD5 failed for {file_state.filename}: {e}",
+                    {"file": file_state.filename, "error": str(e)},
+                )
+
+        with ThreadPoolExecutor(max_workers=4) as executor:
+            executor.map(compute_file_md5, job.files)
+
+        if job.cancelled:
+            self._finalize_cancelled(job, progress_callback)
+            return True
+
+        # Phase 2: Fetch S3 ETags and compare
+        try:
+            s3_client = create_s3_client(aws_profile, aws_region)
+        except Exception as e:
+            with job.lock:
+                job.status = "failed"
+                job.completed_at = datetime.now(UTC).isoformat()
+            log.error(
+                "delete",
+                "s3_client_failed",
+                f"Failed to create S3 client: {e}",
+                {"error": str(e)},
+            )
+            if progress_callback:
+                progress_callback(job)
+            return True
+
+        def verify_against_s3(file_state: FileDeleteState) -> None:
+            """Verify a file against S3 using HEAD + size (primary) and MD5 (secondary).
+
+            Verification levels:
+            - "md5+size": S3 exists, size matches, MD5 matches ETag (single-part)
+            - "size": S3 exists, size matches, multipart ETag (MD5 not comparable)
+            """
+            if job.cancelled:
+                return
+            if file_state.status == DeleteStatus.FAILED:
+                return
+
+            try:
+                metadata = get_object_metadata(
+                    s3_client, file_state.s3_bucket, file_state.s3_path
+                )
+                if not metadata["success"]:
+                    with job.lock:
+                        file_state.status = DeleteStatus.FAILED
+                        file_state.error_message = (
+                            f"S3 object not found: {metadata.get('error', 'unknown')}"
+                        )
+                    return
+
+                s3_size = int(metadata["size"])
+                etag = str(metadata["etag"])
+                file_state.s3_etag = etag
+                file_state.s3_size = s3_size
+
+                # Primary check: file size must match
+                if s3_size != file_state.file_size:
+                    with job.lock:
+                        file_state.status = DeleteStatus.MISMATCH
+                        file_state.error_message = (
+                            f"Size mismatch: local={file_state.file_size}, s3={s3_size}"
+                        )
+                    return
+
+                # Secondary check: MD5 vs ETag (only possible for single-part uploads)
+                if is_multipart_etag(etag):
+                    # Multipart ETag — can't compare MD5, but size is confirmed
+                    with job.lock:
+                        file_state.status = DeleteStatus.VERIFIED
+                        file_state.verification = "size"
+                else:
+                    # Single-part ETag — compare MD5
+                    if etag == file_state.local_md5:
+                        with job.lock:
+                            file_state.status = DeleteStatus.VERIFIED
+                            file_state.verification = "md5+size"
+                    else:
+                        with job.lock:
+                            file_state.status = DeleteStatus.MISMATCH
+                            file_state.error_message = (
+                                f"MD5 mismatch: local={file_state.local_md5}, s3={etag}"
+                            )
+            except Exception as e:
+                with job.lock:
+                    file_state.status = DeleteStatus.FAILED
+                    file_state.error_message = f"S3 verification failed: {e}"
+
+            if progress_callback:
+                progress_callback(job)
+
+        with ThreadPoolExecutor(max_workers=4) as executor:
+            executor.map(verify_against_s3, job.files)
+
+        if job.cancelled:
+            self._finalize_cancelled(job, progress_callback)
+            return True
+
+        # Phase 3: Delete verified files (sequential)
+        with job.lock:
+            job.status = "deleting"
+        if progress_callback:
+            progress_callback(job)
+
+        for file_state in job.files:
+            if job.cancelled:
+                self._finalize_cancelled(job, progress_callback)
+                return True
+
+            if file_state.status != DeleteStatus.VERIFIED:
+                continue
+
+            with job.lock:
+                file_state.status = DeleteStatus.DELETING
+            if progress_callback:
+                progress_callback(job)
+
+            try:
+                os.unlink(file_state.local_path)
+                with job.lock:
+                    file_state.status = DeleteStatus.DELETED
+                log.info(
+                    "delete",
+                    "file_deleted",
+                    f"Deleted {file_state.filename}",
+                    {
+                        "file": file_state.filename,
+                        "local_path": file_state.local_path,
+                        "s3_path": file_state.s3_path,
+                        "size": file_state.file_size,
+                    },
+                )
+            except Exception as e:
+                with job.lock:
+                    file_state.status = DeleteStatus.FAILED
+                    file_state.error_message = f"Delete failed: {e}"
+                log.error(
+                    "delete",
+                    "delete_failed",
+                    f"Failed to delete {file_state.filename}: {e}",
+                    {"file": file_state.filename, "error": str(e)},
+                )
+
+            if progress_callback:
+                progress_callback(job)
+
+        # Finalize
+        with job.lock:
+            job.status = "completed"
+            job.completed_at = datetime.now(UTC).isoformat()
+
+        log.info(
+            "delete",
+            "job_completed",
+            f"Delete job completed: {job.to_progress_dict()['status_counts']}",
+            {"job_id": job_id, **job.to_progress_dict()["status_counts"]},
+        )
+
+        if progress_callback:
+            progress_callback(job)
+
+        return True
+
+    def _finalize_cancelled(
+        self,
+        job: DeleteJob,
+        progress_callback: Callable[[DeleteJob], None] | None,
+    ) -> None:
+        """Mark remaining pending/verifying files as cancelled and finalize."""
+        with job.lock:
+            for f in job.files:
+                if f.status in (
+                    DeleteStatus.PENDING,
+                    DeleteStatus.VERIFYING,
+                    DeleteStatus.VERIFIED,
+                ):
+                    f.status = DeleteStatus.CANCELLED
+            job.status = "cancelled"
+            job.completed_at = datetime.now(UTC).isoformat()
+
+        log = get_log_service()
+        log.info(
+            "delete",
+            "job_cancelled",
+            "Delete job cancelled",
+            {"job_id": job.job_id},
+        )
+
+        if progress_callback:
+            progress_callback(job)
+
+    def cancel_job(self, job_id: str) -> bool:
+        """Cancel a delete job.
+
+        Args:
+            job_id: The job to cancel
+
+        Returns:
+            True if job was found and cancelled
+        """
+        job = self.jobs.get(job_id)
+        if not job:
+            return False
+        job.cancelled = True
+        return True
+
+    def get_job(self, job_id: str) -> DeleteJob | None:
+        """Retrieve a delete job by ID."""
+        return self.jobs.get(job_id)
+
+
+# Global singleton
+_delete_manager: DeleteManager | None = None
+
+
+def get_delete_manager() -> DeleteManager:
+    """Get the global delete manager instance."""
+    global _delete_manager
+    if _delete_manager is None:
+        _delete_manager = DeleteManager()
+    return _delete_manager

From b11d77bcb7e15177152dedb2e5b620bb04e4061b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:45:09 -0700
Subject: [PATCH 028/173] Ignore: Add frontend reactjs tsx ignore

---
 frontend/.gitignore | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 frontend/.gitignore

diff --git a/frontend/.gitignore b/frontend/.gitignore
new file mode 100644
index 0000000..a547bf3
--- /dev/null
+++ b/frontend/.gitignore
@@ -0,0 +1,24 @@
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+lerna-debug.log*
+
+node_modules
+dist
+dist-ssr
+*.local
+
+# Editor directories and files
+.vscode/*
+!.vscode/extensions.json
+.idea
+.DS_Store
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?

From 09355e562d8a0308279828aea35dcb70b0fae13d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:48:47 -0700
Subject: [PATCH 029/173] Ignore: Add more typescript/vite options

---
 frontend/.gitignore | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/frontend/.gitignore b/frontend/.gitignore
index a547bf3..982baa9 100644
--- a/frontend/.gitignore
+++ b/frontend/.gitignore
@@ -7,11 +7,32 @@ yarn-error.log*
 pnpm-debug.log*
 lerna-debug.log*
 
+# Dependencies
 node_modules
+
+# Build outputs
 dist
 dist-ssr
 *.local
 
+# Environment variables
+.env
+.env.local
+.env.*.local
+
+# Testing
+coverage
+.vitest
+
+# TypeScript
+*.tsbuildinfo
+*.tsbuildinfo.*
+
+# Caches
+.cache
+.vite
+.biome-cache
+
 # Editor directories and files
 .vscode/*
 !.vscode/extensions.json
@@ -22,3 +43,6 @@ dist-ssr
 *.njsproj
 *.sln
 *.sw?
+
+# OS files
+Thumbs.db

From ee6431f4027fa38859fd2643128440073cb80fda Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:49:06 -0700
Subject: [PATCH 030/173] Frontend: Init package

---
 frontend/package-lock.json | 5538 ++++++++++++++++++++++++++++++++++++
 frontend/package.json      |   47 +
 2 files changed, 5585 insertions(+)
 create mode 100644 frontend/package-lock.json
 create mode 100644 frontend/package.json

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
new file mode 100644
index 0000000..c7aefc7
--- /dev/null
+++ b/frontend/package-lock.json
@@ -0,0 +1,5538 @@
+{
+  "name": "frontend",
+  "version": "0.0.0",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "frontend",
+      "version": "0.0.0",
+      "dependencies": {
+        "@tanstack/react-table": "^8.21.3",
+        "@tanstack/react-virtual": "^3.13.18",
+        "lucide-react": "^0.574.0",
+        "react": "^19.2.0",
+        "react-dom": "^19.2.0",
+        "react-router-dom": "^7.13.0",
+        "zustand": "^5.0.11"
+      },
+      "devDependencies": {
+        "@eslint/js": "^9.39.1",
+        "@tailwindcss/vite": "^4.1.18",
+        "@testing-library/jest-dom": "^6.9.1",
+        "@testing-library/react": "^16.3.2",
+        "@testing-library/user-event": "^14.6.1",
+        "@types/node": "^24.10.1",
+        "@types/react": "^19.2.7",
+        "@types/react-dom": "^19.2.3",
+        "@vitejs/plugin-react": "^5.1.1",
+        "@vitest/coverage-v8": "^4.0.18",
+        "eslint": "^9.39.1",
+        "eslint-plugin-react-hooks": "^7.0.1",
+        "eslint-plugin-react-refresh": "^0.4.24",
+        "globals": "^16.5.0",
+        "jsdom": "^27.0.1",
+        "tailwindcss": "^4.1.18",
+        "typescript": "~5.9.3",
+        "typescript-eslint": "^8.48.0",
+        "vite": "^7.3.1",
+        "vitest": "^3.2.4"
+      }
+    },
+    "node_modules/@adobe/css-tools": {
+      "version": "4.4.4",
+      "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.4.4.tgz",
+      "integrity": "sha512-Elp+iwUx5rN5+Y8xLt5/GRoG20WGoDCQ/1Fb+1LiGtvwbDavuSk0jhD/eZdckHAuzcDzccnkv+rEjyWfRx18gg==",
+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/@asamuzakjp/css-color": {
+      "version": "4.1.2",
+      "resolved": "https://registry.npmjs.org/@asamuzakjp/css-color/-/css-color-4.1.2.tgz",
+      "integrity": "sha512-NfBUvBaYgKIuq6E/RBLY1m0IohzNHAYyaJGuTK79Z23uNwmz2jl1mPsC5ZxCCxylinKhT1Amn5oNTlx1wN8cQg==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@csstools/css-calc": "^3.0.0",
+        "@csstools/css-color-parser": "^4.0.1",
+        "@csstools/css-parser-algorithms": "^4.0.0",
+        "@csstools/css-tokenizer": "^4.0.0",
+        "lru-cache": "^11.2.5"
+      }
+    },
+    "node_modules/@asamuzakjp/css-color/node_modules/lru-cache": {
+      "version": "11.2.6",
+      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.6.tgz",
+      "integrity": "sha512-ESL2CrkS/2wTPfuend7Zhkzo2u0daGJ/A2VucJOgQ/C48S/zB8MMeMHSGKYpXhIjbPxfuezITkaBH1wqv00DDQ==",
+      "dev": true,
+      "license": "BlueOak-1.0.0",
+      "engines": {
+        "node": "20 || >=22"
+      }
+    },
+    "node_modules/@asamuzakjp/dom-selector": {
+      "version": "6.8.1",
+      "resolved": "https://registry.npmjs.org/@asamuzakjp/dom-selector/-/dom-selector-6.8.1.tgz",
+      "integrity": "sha512-MvRz1nCqW0fsy8Qz4dnLIvhOlMzqDVBabZx6lH+YywFDdjXhMY37SmpV1XFX3JzG5GWHn63j6HX6QPr3lZXHvQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@asamuzakjp/nwsapi": "^2.3.9",
+        "bidi-js": "^1.0.3",
+        "css-tree": "^3.1.0",
+        "is-potential-custom-element-name": "^1.0.1",
+        "lru-cache": "^11.2.6"
+      }
+    },
+    "node_modules/@asamuzakjp/dom-selector/node_modules/lru-cache": {
+      "version": "11.2.6",
+      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.6.tgz",
+      "integrity": "sha512-ESL2CrkS/2wTPfuend7Zhkzo2u0daGJ/A2VucJOgQ/C48S/zB8MMeMHSGKYpXhIjbPxfuezITkaBH1wqv00DDQ==",
+      "dev": true,
+      "license": "BlueOak-1.0.0",
+      "engines": {
+        "node": "20 || >=22"
+      }
+    },
+    "node_modules/@asamuzakjp/nwsapi": {
+      "version": "2.3.9",
+      "resolved": "https://registry.npmjs.org/@asamuzakjp/nwsapi/-/nwsapi-2.3.9.tgz",
+      "integrity": "sha512-n8GuYSrI9bF7FFZ/SjhwevlHc8xaVlb/7HmHelnc/PZXBD2ZR49NnN9sMMuDdEGPeeRQ5d0hqlSlEpgCX3Wl0Q==",
+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/@babel/code-frame": {
+      "version": "7.29.0",
+      "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.0.tgz",
+      "integrity": "sha512-9NhCeYjq9+3uxgdtp20LSiJXJvN0FeCtNGpJxuMFZ1Kv3cWUNb6DOhJwUvcVCzKGR66cw4njwM6hrJLqgOwbcw==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@babel/helper-validator-identifier": "^7.28.5",
+        "js-tokens": "^4.0.0",
+        "picocolors": "^1.1.1"
+      },
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
+    "node_modules/@babel/compat-data": {
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+      "integrity": "sha512-T1NCJqT/j9+cn8fvkt7jtwbLBfLC/1y1c7NtCeXFRgzGTsafi68MRv8yzkYSapBnFA6L3U2VSc02ciDzoAJhJg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
+    "node_modules/@babel/core": {
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+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.29.0.tgz",
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+      "dev": true,
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+        "node": ">=6.9.0"
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+      "funding": {
+        "type": "opencollective",
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+      "license": "MIT",
+      "dependencies": {
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+        "@babel/types": "^7.29.0",
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+        "@jridgewell/trace-mapping": "^0.3.28",
+        "jsesc": "^3.0.2"
+      },
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+      "license": "MIT",
+      "dependencies": {
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+        "@babel/helper-validator-option": "^7.27.1",
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+        "semver": "^6.3.1"
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+        "node": ">=6.9.0"
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+    },
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+      "resolved": "https://registry.npmjs.org/@babel/helper-globals/-/helper-globals-7.28.0.tgz",
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+      "license": "MIT",
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
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+    "node_modules/whatwg-encoding": {
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+      "deprecated": "Use @exodus/bytes instead for a more spec-conformant and faster implementation",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "iconv-lite": "0.6.3"
+      },
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/whatwg-mimetype": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-4.0.0.tgz",
+      "integrity": "sha512-QaKxh0eNIi2mE9p2vEdzfagOKHCcj1pJ56EEHGQOVxp8r9/iszLUUV7v89x9O1p/T+NlTM5W7jW6+cz4Fq1YVg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/whatwg-url": {
+      "version": "15.1.0",
+      "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-15.1.0.tgz",
+      "integrity": "sha512-2ytDk0kiEj/yu90JOAp44PVPUkO9+jVhyf+SybKlRHSDlvOOZhdPIrr7xTH64l4WixO2cP+wQIcgujkGBPPz6g==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "tr46": "^6.0.0",
+        "webidl-conversions": "^8.0.0"
+      },
+      "engines": {
+        "node": ">=20"
+      }
+    },
+    "node_modules/which": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
+      "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
+      "dev": true,
+      "license": "ISC",
+      "dependencies": {
+        "isexe": "^2.0.0"
+      },
+      "bin": {
+        "node-which": "bin/node-which"
+      },
+      "engines": {
+        "node": ">= 8"
+      }
+    },
+    "node_modules/why-is-node-running": {
+      "version": "2.3.0",
+      "resolved": "https://registry.npmjs.org/why-is-node-running/-/why-is-node-running-2.3.0.tgz",
+      "integrity": "sha512-hUrmaWBdVDcxvYqnyh09zunKzROWjbZTiNy8dBEjkS7ehEDQibXJ7XvlmtbwuTclUiIyN+CyXQD4Vmko8fNm8w==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "siginfo": "^2.0.0",
+        "stackback": "0.0.2"
+      },
+      "bin": {
+        "why-is-node-running": "cli.js"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
+    "node_modules/word-wrap": {
+      "version": "1.2.5",
+      "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz",
+      "integrity": "sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/ws": {
+      "version": "8.19.0",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.19.0.tgz",
+      "integrity": "sha512-blAT2mjOEIi0ZzruJfIhb3nps74PRWTCz1IjglWEEpQl5XS/UNama6u2/rjFkDDouqr4L67ry+1aGIALViWjDg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=10.0.0"
+      },
+      "peerDependencies": {
+        "bufferutil": "^4.0.1",
+        "utf-8-validate": ">=5.0.2"
+      },
+      "peerDependenciesMeta": {
+        "bufferutil": {
+          "optional": true
+        },
+        "utf-8-validate": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/xml-name-validator": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-5.0.0.tgz",
+      "integrity": "sha512-EvGK8EJ3DhaHfbRlETOWAS5pO9MZITeauHKJyb8wyajUfQUenkIg2MvLDTZ4T/TgIcm3HU0TFBgWWboAZ30UHg==",
+      "dev": true,
+      "license": "Apache-2.0",
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/xmlchars": {
+      "version": "2.2.0",
+      "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz",
+      "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==",
+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/yallist": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz",
+      "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==",
+      "dev": true,
+      "license": "ISC"
+    },
+    "node_modules/yocto-queue": {
+      "version": "0.1.0",
+      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+      "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/zod": {
+      "version": "4.3.6",
+      "resolved": "https://registry.npmjs.org/zod/-/zod-4.3.6.tgz",
+      "integrity": "sha512-rftlrkhHZOcjDwkGlnUtZZkvaPHCsDATp4pGpuOOMDaTdDDXF91wuVDJoWoPsKX/3YPQ5fHuF3STjcYyKr+Qhg==",
+      "dev": true,
+      "license": "MIT",
+      "funding": {
+        "url": "https://github.com/sponsors/colinhacks"
+      }
+    },
+    "node_modules/zod-validation-error": {
+      "version": "4.0.2",
+      "resolved": "https://registry.npmjs.org/zod-validation-error/-/zod-validation-error-4.0.2.tgz",
+      "integrity": "sha512-Q6/nZLe6jxuU80qb/4uJ4t5v2VEZ44lzQjPDhYJNztRQ4wyWc6VF3D3Kb/fAuPetZQnhS3hnajCf9CsWesghLQ==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=18.0.0"
+      },
+      "peerDependencies": {
+        "zod": "^3.25.0 || ^4.0.0"
+      }
+    },
+    "node_modules/zustand": {
+      "version": "5.0.11",
+      "resolved": "https://registry.npmjs.org/zustand/-/zustand-5.0.11.tgz",
+      "integrity": "sha512-fdZY+dk7zn/vbWNCYmzZULHRrss0jx5pPFiOuMZ/5HJN6Yv3u+1Wswy/4MpZEkEGhtNH+pwxZB8OKgUBPzYAGg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12.20.0"
+      },
+      "peerDependencies": {
+        "@types/react": ">=18.0.0",
+        "immer": ">=9.0.6",
+        "react": ">=18.0.0",
+        "use-sync-external-store": ">=1.2.0"
+      },
+      "peerDependenciesMeta": {
+        "@types/react": {
+          "optional": true
+        },
+        "immer": {
+          "optional": true
+        },
+        "react": {
+          "optional": true
+        },
+        "use-sync-external-store": {
+          "optional": true
+        }
+      }
+    }
+  }
+}
diff --git a/frontend/package.json b/frontend/package.json
new file mode 100644
index 0000000..ec763b6
--- /dev/null
+++ b/frontend/package.json
@@ -0,0 +1,47 @@
+{
+  "name": "frontend",
+  "private": true,
+  "version": "0.0.0",
+  "type": "module",
+  "scripts": {
+    "dev": "vite",
+    "build": "tsc -b && vite build",
+    "preview": "vite preview",
+    "typecheck": "tsc -b --noEmit",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
+    "check": "tsc -b --noEmit && vitest run"
+  },
+  "dependencies": {
+    "@tanstack/react-table": "^8.21.3",
+    "@tanstack/react-virtual": "^3.13.18",
+    "lucide-react": "^0.574.0",
+    "react": "^19.2.0",
+    "react-dom": "^19.2.0",
+    "react-router-dom": "^7.13.0",
+    "zustand": "^5.0.11"
+  },
+  "devDependencies": {
+    "@eslint/js": "^9.39.1",
+    "@tailwindcss/vite": "^4.1.18",
+    "@testing-library/jest-dom": "^6.9.1",
+    "@testing-library/react": "^16.3.2",
+    "@testing-library/user-event": "^14.6.1",
+    "@types/node": "^24.10.1",
+    "@types/react": "^19.2.7",
+    "@types/react-dom": "^19.2.3",
+    "@vitejs/plugin-react": "^5.1.1",
+    "@vitest/coverage-v8": "^4.0.18",
+    "eslint": "^9.39.1",
+    "eslint-plugin-react-hooks": "^7.0.1",
+    "eslint-plugin-react-refresh": "^0.4.24",
+    "globals": "^16.5.0",
+    "jsdom": "^27.0.1",
+    "tailwindcss": "^4.1.18",
+    "typescript": "~5.9.3",
+    "typescript-eslint": "^8.48.0",
+    "vite": "^7.3.1",
+    "vitest": "^3.2.4"
+  }
+}

From 043d7c47ab5444d8ecde20611db21ceab51ef631 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:49:27 -0700
Subject: [PATCH 031/173] Frontend: Enable linting

---
 frontend/eslint.config.js | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 frontend/eslint.config.js

diff --git a/frontend/eslint.config.js b/frontend/eslint.config.js
new file mode 100644
index 0000000..5e6b472
--- /dev/null
+++ b/frontend/eslint.config.js
@@ -0,0 +1,23 @@
+import js from '@eslint/js'
+import globals from 'globals'
+import reactHooks from 'eslint-plugin-react-hooks'
+import reactRefresh from 'eslint-plugin-react-refresh'
+import tseslint from 'typescript-eslint'
+import { defineConfig, globalIgnores } from 'eslint/config'
+
+export default defineConfig([
+  globalIgnores(['dist']),
+  {
+    files: ['**/*.{ts,tsx}'],
+    extends: [
+      js.configs.recommended,
+      tseslint.configs.recommended,
+      reactHooks.configs.flat.recommended,
+      reactRefresh.configs.vite,
+    ],
+    languageOptions: {
+      ecmaVersion: 2020,
+      globals: globals.browser,
+    },
+  },
+])

From 61353767ae2ae6f25d7cc230fb47c231885155ff Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:49:49 -0700
Subject: [PATCH 032/173] Frontend: Configure typescript

---
 frontend/tsconfig.app.json  | 28 ++++++++++++++++++++++++++++
 frontend/tsconfig.json      |  7 +++++++
 frontend/tsconfig.node.json | 26 ++++++++++++++++++++++++++
 3 files changed, 61 insertions(+)
 create mode 100644 frontend/tsconfig.app.json
 create mode 100644 frontend/tsconfig.json
 create mode 100644 frontend/tsconfig.node.json

diff --git a/frontend/tsconfig.app.json b/frontend/tsconfig.app.json
new file mode 100644
index 0000000..a9b5a59
--- /dev/null
+++ b/frontend/tsconfig.app.json
@@ -0,0 +1,28 @@
+{
+  "compilerOptions": {
+    "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.app.tsbuildinfo",
+    "target": "ES2022",
+    "useDefineForClassFields": true,
+    "lib": ["ES2022", "DOM", "DOM.Iterable"],
+    "module": "ESNext",
+    "types": ["vite/client"],
+    "skipLibCheck": true,
+
+    /* Bundler mode */
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "verbatimModuleSyntax": true,
+    "moduleDetection": "force",
+    "noEmit": true,
+    "jsx": "react-jsx",
+
+    /* Linting */
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "erasableSyntaxOnly": true,
+    "noFallthroughCasesInSwitch": true,
+    "noUncheckedSideEffectImports": true
+  },
+  "include": ["src"]
+}
diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json
new file mode 100644
index 0000000..1ffef60
--- /dev/null
+++ b/frontend/tsconfig.json
@@ -0,0 +1,7 @@
+{
+  "files": [],
+  "references": [
+    { "path": "./tsconfig.app.json" },
+    { "path": "./tsconfig.node.json" }
+  ]
+}
diff --git a/frontend/tsconfig.node.json b/frontend/tsconfig.node.json
new file mode 100644
index 0000000..8a67f62
--- /dev/null
+++ b/frontend/tsconfig.node.json
@@ -0,0 +1,26 @@
+{
+  "compilerOptions": {
+    "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.node.tsbuildinfo",
+    "target": "ES2023",
+    "lib": ["ES2023"],
+    "module": "ESNext",
+    "types": ["node"],
+    "skipLibCheck": true,
+
+    /* Bundler mode */
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "verbatimModuleSyntax": true,
+    "moduleDetection": "force",
+    "noEmit": true,
+
+    /* Linting */
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "erasableSyntaxOnly": true,
+    "noFallthroughCasesInSwitch": true,
+    "noUncheckedSideEffectImports": true
+  },
+  "include": ["vite.config.ts"]
+}

From ce06ec95347d73713cde256a134f18d86e9cea03 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:50:20 -0700
Subject: [PATCH 033/173] Frontend: Configure vite

---
 frontend/vite.config.ts | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 frontend/vite.config.ts

diff --git a/frontend/vite.config.ts b/frontend/vite.config.ts
new file mode 100644
index 0000000..fdadc3d
--- /dev/null
+++ b/frontend/vite.config.ts
@@ -0,0 +1,19 @@
+import tailwindcss from "@tailwindcss/vite";
+import react from "@vitejs/plugin-react";
+import { defineConfig } from "vite";
+
+export default defineConfig({
+  plugins: [react(), tailwindcss()],
+  server: {
+    port: 3000,
+    proxy: {
+      "/api": {
+        target: "http://localhost:5000",
+        changeOrigin: true,
+      },
+    },
+  },
+  build: {
+    outDir: "dist",
+  },
+});

From 3dce849fed5b492a94c02af8211ffc18e9da268f Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:50:44 -0700
Subject: [PATCH 034/173] Frontend: Add entrypoint index

---
 frontend/index.html | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 frontend/index.html

diff --git a/frontend/index.html b/frontend/index.html
new file mode 100644
index 0000000..c10691f
--- /dev/null
+++ b/frontend/index.html
@@ -0,0 +1,17 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <link rel="icon" type="image/png" href="/images/modaq-logo.png" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <link
+      href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700&display=swap"
+      rel="stylesheet"
+    />
+    <title>MODAQ Upload</title>
+  </head>
+  <body>
+    <div id="root"></div>
+    <script type="module" src="/src/main.tsx"></script>
+  </body>
+</html>

From 45d0d3a0d66b887960a55759312916f6c309577a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:51:04 -0700
Subject: [PATCH 035/173] Frontend: Add NLR assets

---
 .../public/images/alliance-logo_black.svg     |  59 +++
 frontend/public/images/doe-logo.svg           | 339 ++++++++++++++++++
 frontend/public/images/modaq-logo.png         | Bin 0 -> 3833 bytes
 frontend/public/images/nlr-logo@2x-01.png     | Bin 0 -> 23341 bytes
 4 files changed, 398 insertions(+)
 create mode 100644 frontend/public/images/alliance-logo_black.svg
 create mode 100644 frontend/public/images/doe-logo.svg
 create mode 100644 frontend/public/images/modaq-logo.png
 create mode 100644 frontend/public/images/nlr-logo@2x-01.png

diff --git a/frontend/public/images/alliance-logo_black.svg b/frontend/public/images/alliance-logo_black.svg
new file mode 100644
index 0000000..be59986
--- /dev/null
+++ b/frontend/public/images/alliance-logo_black.svg
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg id="Layer_1" data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" version="1.1" viewBox="0 0 340.7 123.6">
+  <defs>
+    <style>
+      .cls-1 {
+        fill: #cdcdcd;
+      }
+
+      .cls-1, .cls-2, .cls-3 {
+        stroke-width: 0px;
+      }
+
+      .cls-1, .cls-3 {
+        fill-rule: evenodd;
+      }
+
+      .cls-2, .cls-3 {
+        fill: #231f20;
+      }
+    </style>
+  </defs>
+  <g>
+    <path class="cls-3" d="M55.1,77.5l1.5,5.6h4.8l-6.1-21.8h-5.8l-6,21.8h4.6l1.4-5.6h5.6ZM50.1,73.8l1.2-4.6c.3-1.3.6-2.9.9-4.2h0c.3,1.3.6,2.9,1,4.2l1.2,4.6h-4.3Z"/>
+    <rect class="cls-2" x="63.4" y="60.1" width="4.4" height="23"/>
+    <rect class="cls-2" x="71.1" y="60.1" width="4.4" height="23"/>
+    <path class="cls-3" d="M83.2,83.1v-15.8h-4.4v15.8h4.4ZM81,60.4c-1.4,0-2.4,1.1-2.3,2.5,0,1.4.9,2.5,2.3,2.5s2.4-1.1,2.4-2.5c0-1.4-.9-2.5-2.4-2.5Z"/>
+    <path class="cls-3" d="M98.4,73.7c0-3.7-1.5-6.8-6.3-6.8s-4.5.8-5.5,1.4l.8,3.2c.9-.6,2.5-1.2,3.9-1.2,2.2,0,2.6,1.2,2.6,2v.2c-5,0-8.4,1.9-8.4,6s1.7,4.8,4.6,4.8,3.1-.7,4.1-1.9h0l.3,1.6h4c-.1-.9-.2-2.3-.2-3.8v-5.5ZM94.1,77.3c0,.3,0,.6,0,.8-.3,1-1.2,1.8-2.3,1.8s-1.7-.6-1.7-1.9c0-1.9,1.8-2.5,4.1-2.5v1.7Z"/>
+    <path class="cls-3" d="M101.6,83.1h4.4v-9.1c0-.5,0-.9.2-1.2.3-.9,1-1.8,2.2-1.8s2.2,1.4,2.2,3.4v8.8h4.4v-9.4c0-4.7-2.2-6.8-5.1-6.8s-3.8,1.5-4.4,2.5h0l-.2-2.2h-3.8c0,1.4.1,3.1.1,5v10.8Z"/>
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diff --git a/frontend/public/images/doe-logo.svg b/frontend/public/images/doe-logo.svg
new file mode 100644
index 0000000..7075378
--- /dev/null
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From cb6529517a322de2d815906c3490c3f851f31333 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:52:21 -0700
Subject: [PATCH 036/173] Frontend: Add baseline NLR/tailwind css

---
 frontend/src/index.css | 186 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 186 insertions(+)
 create mode 100644 frontend/src/index.css

diff --git a/frontend/src/index.css b/frontend/src/index.css
new file mode 100644
index 0000000..6dc8e85
--- /dev/null
+++ b/frontend/src/index.css
@@ -0,0 +1,186 @@
+@import "tailwindcss";
+
+/* ── NLR Brand Colors (Tailwind v4 @theme) ── */
+@theme {
+  --color-nlr-blue: #0079C2;
+  --color-nlr-blue-light: #00A3E4;
+  --color-nlr-yellow: #EE9521;
+  --color-nlr-yellow-light: #FFC423;
+  --color-nlr-green: #5D9732;
+  --color-nlr-green-light: #9ECE42;
+  --color-nlr-gray: #5E6A71;
+  --color-nlr-gray-light: #D1D5D8;
+  --color-nlr-gray-bg: #EDEDED;
+  --color-nlr-gray-footer: #E3E6E8;
+  --color-nlr-text: #212224;
+  --font-family-roboto: "Roboto", "Helvetica Neue", Helvetica, sans-serif;
+}
+
+/* ── Base ── */
+body {
+  font-family: var(--font-family-roboto);
+}
+
+/* ── NLR Header ── */
+.nlr-header {
+  background: #fff;
+  width: 100%;
+}
+
+.nlr-header-top {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+  height: 100px;
+  max-width: 1140px;
+  margin: 0 auto;
+  padding: 0 15px;
+}
+
+.nlr-header-title {
+  font-weight: normal;
+  color: #212224;
+  font-size: 24px;
+  letter-spacing: 0.5px;
+}
+
+.nlr-logo-image {
+  width: 200px;
+}
+
+/* ── Menu bar ── */
+.nlr-menu-bar {
+  background: #EDEDED;
+  border-top: 1px solid #D6D4D4;
+  height: 50px;
+}
+
+.nlr-menu-container {
+  max-width: 1140px;
+  margin: 0 auto;
+  display: flex;
+  align-items: center;
+  height: 100%;
+  padding: 0 15px;
+}
+
+.nlr-menu-item {
+  color: #2F2F2F;
+  padding: 14px 20px;
+  font-size: 14px;
+  text-decoration: none;
+  transition: all 0.2s;
+}
+
+.nlr-menu-item:hover,
+.nlr-menu-item.active {
+  background: #5E6A71;
+  color: #fff;
+}
+
+/* ── NLR Footer ── */
+.nlr-footer {
+  background-color: #E3E6E8;
+  font-size: 14px;
+  font-weight: 400;
+  line-height: 1.2;
+}
+
+.nlr-footer-top {
+  background-color: #D1D5D8;
+  padding: 1.5em 0;
+}
+
+.nlr-footer-bottom {
+  padding: 1.5em 0 3em 0;
+}
+
+.nlr-footer a {
+  color: #000;
+  text-decoration: none;
+}
+
+.nlr-footer a:hover {
+  color: #C60;
+  text-decoration: underline;
+}
+
+.nlr-attr {
+  font-size: 12px;
+}
+
+/* ── Scrollbar-hide utility ── */
+.scrollbar-hide {
+  -ms-overflow-style: none;
+  scrollbar-width: none;
+}
+.scrollbar-hide::-webkit-scrollbar {
+  display: none;
+}
+
+/* ── Drag and drop ── */
+.drop-zone {
+  transition: all 0.3s ease;
+}
+
+.drop-zone.drag-over {
+  border-color: #0079C2;
+  background-color: rgba(0, 121, 194, 0.1);
+}
+
+/* ── Progress bar animation ── */
+.progress-bar {
+  transition: width 0.4s ease-out;
+}
+
+/* ── File item hover ── */
+.file-item:hover {
+  background-color: rgba(0, 121, 194, 0.05);
+}
+
+/* ── Spinner ── */
+@keyframes spin {
+  to { transform: rotate(360deg); }
+}
+
+.spinner {
+  animation: spin 1s linear infinite;
+}
+
+/* ── Step indicator transitions ── */
+.step-circle,
+.step-label,
+.step-connector {
+  transition: all 0.3s ease;
+}
+
+/* ── Responsive ── */
+@media (max-width: 991px) {
+  .nlr-header-top,
+  .nlr-menu-container {
+    max-width: 720px;
+  }
+}
+
+@media (max-width: 767px) {
+  .nlr-header-top {
+    flex-direction: column;
+    height: auto;
+    padding: 15px;
+    text-align: center;
+  }
+
+  .nlr-header-title {
+    font-size: 20px;
+    margin-top: 10px;
+  }
+
+  .nlr-logo-image {
+    width: 180px;
+  }
+
+  .nlr-menu-item {
+    padding: 12px 15px;
+    font-size: 13px;
+  }
+}

From 7ac629c8e4121b6907dcc77bf6693604ece9373c Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:52:54 -0700
Subject: [PATCH 037/173] Frontend: Add tsx entry point

---
 frontend/src/App.tsx  | 31 +++++++++++++++++++++++++++++++
 frontend/src/main.tsx | 13 +++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 frontend/src/App.tsx
 create mode 100644 frontend/src/main.tsx

diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
new file mode 100644
index 0000000..b7ccc87
--- /dev/null
+++ b/frontend/src/App.tsx
@@ -0,0 +1,31 @@
+import { useEffect } from "react";
+import { Route, Routes } from "react-router-dom";
+import Layout from "./components/layout/Layout.tsx";
+import DeletePage from "./pages/DeletePage.tsx";
+import FilesPage from "./pages/FilesPage.tsx";
+import LogsPage from "./pages/LogsPage.tsx";
+import SettingsPage from "./pages/SettingsPage.tsx";
+import UploadPage from "./pages/UploadPage.tsx";
+import { useAppStore } from "./stores/appStore.ts";
+
+export default function App() {
+  const loadSettings = useAppStore((s) => s.loadSettings);
+  const loadVersion = useAppStore((s) => s.loadVersion);
+
+  useEffect(() => {
+    loadSettings();
+    loadVersion();
+  }, [loadSettings, loadVersion]);
+
+  return (
+    <Routes>
+      <Route element={<Layout />}>
+        <Route index element={<UploadPage />} />
+        <Route path="delete" element={<DeletePage />} />
+        <Route path="files" element={<FilesPage />} />
+        <Route path="logs" element={<LogsPage />} />
+        <Route path="settings" element={<SettingsPage />} />
+      </Route>
+    </Routes>
+  );
+}
diff --git a/frontend/src/main.tsx b/frontend/src/main.tsx
new file mode 100644
index 0000000..a721344
--- /dev/null
+++ b/frontend/src/main.tsx
@@ -0,0 +1,13 @@
+import { StrictMode } from "react";
+import { createRoot } from "react-dom/client";
+import { BrowserRouter } from "react-router-dom";
+import App from "./App.tsx";
+import "./index.css";
+
+createRoot(document.getElementById("root")!).render(
+  <StrictMode>
+    <BrowserRouter>
+      <App />
+    </BrowserRouter>
+  </StrictMode>,
+);

From fd8ac4d8ff6a95fd22063b0aeaf785063d0318c3 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 14:55:12 -0700
Subject: [PATCH 038/173] Frontend: Add api request/response functions

---
 frontend/src/api/client.ts | 42 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 frontend/src/api/client.ts

diff --git a/frontend/src/api/client.ts b/frontend/src/api/client.ts
new file mode 100644
index 0000000..f0ba620
--- /dev/null
+++ b/frontend/src/api/client.ts
@@ -0,0 +1,42 @@
+/** Typed fetch wrappers for the Flask API. */
+
+export class ApiError extends Error {
+  status: number;
+  constructor(status: number, message: string) {
+    super(message);
+    this.name = "ApiError";
+    this.status = status;
+  }
+}
+
+async function handleResponse<T>(res: Response): Promise<T> {
+  if (!res.ok) {
+    const body = await res.json().catch(() => ({ error: res.statusText }));
+    throw new ApiError(res.status, body.error ?? res.statusText);
+  }
+  return res.json() as Promise<T>;
+}
+
+export async function apiGet<T>(url: string, params?: Record<string, string>): Promise<T> {
+  const qs = params ? `?${new URLSearchParams(params)}` : "";
+  const res = await fetch(`${url}${qs}`);
+  return handleResponse<T>(res);
+}
+
+export async function apiPost<T>(url: string, body?: unknown): Promise<T> {
+  const res = await fetch(url, {
+    method: "POST",
+    headers: body != null ? { "Content-Type": "application/json" } : undefined,
+    body: body != null ? JSON.stringify(body) : undefined,
+  });
+  return handleResponse<T>(res);
+}
+
+export async function apiPut<T>(url: string, body: unknown): Promise<T> {
+  const res = await fetch(url, {
+    method: "PUT",
+    headers: { "Content-Type": "application/json" },
+    body: JSON.stringify(body),
+  });
+  return handleResponse<T>(res);
+}

From 7f2e2ae767750287b93f418d1e971f5d71dd02ff Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:29:27 -0700
Subject: [PATCH 039/173] Frontend: Add byte formatters

---
 frontend/src/utils/format/bytes.ts | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 frontend/src/utils/format/bytes.ts

diff --git a/frontend/src/utils/format/bytes.ts b/frontend/src/utils/format/bytes.ts
new file mode 100644
index 0000000..f6a1799
--- /dev/null
+++ b/frontend/src/utils/format/bytes.ts
@@ -0,0 +1,10 @@
+/**
+ * Format bytes into a human-readable string (e.g., "1.23 GB").
+ */
+export function formatBytes(bytes: number): string {
+  if (bytes === 0) return "0 B";
+  const units = ["B", "KB", "MB", "GB", "TB"];
+  const i = Math.floor(Math.log(bytes) / Math.log(1024));
+  const value = bytes / 1024 ** i;
+  return `${value.toFixed(i === 0 ? 0 : 2)} ${units[i]}`;
+}

From 1026b7b537577e4158d6ac41de76f038f2a0486d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:29:55 -0700
Subject: [PATCH 040/173] Utils: add transfer speed formatters

---
 frontend/src/utils/format/speed.ts | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 frontend/src/utils/format/speed.ts

diff --git a/frontend/src/utils/format/speed.ts b/frontend/src/utils/format/speed.ts
new file mode 100644
index 0000000..ea77e3e
--- /dev/null
+++ b/frontend/src/utils/format/speed.ts
@@ -0,0 +1,7 @@
+/**
+ * Format a speed in Mbps.
+ */
+export function formatSpeed(mbps: number | null): string {
+  if (mbps == null) return "--";
+  return `${mbps.toFixed(2)} Mbps`;
+}

From 3db7e58a30fab8dbf2ca5d306e590cce97573082 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:30:11 -0700
Subject: [PATCH 041/173] Frontend: Add time/duration formatters

---
 frontend/src/utils/format/time.ts | 32 +++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 frontend/src/utils/format/time.ts

diff --git a/frontend/src/utils/format/time.ts b/frontend/src/utils/format/time.ts
new file mode 100644
index 0000000..2faea65
--- /dev/null
+++ b/frontend/src/utils/format/time.ts
@@ -0,0 +1,32 @@
+/**
+ * Format seconds into a human-readable ETA string.
+ * Returns "--" for null/invalid values.
+ */
+export function formatEta(seconds: number | null | undefined): string {
+  if (seconds == null || seconds <= 0) return "--";
+  if (seconds < 60) return `${Math.round(seconds)}s`;
+  if (seconds < 3600) {
+    const m = Math.floor(seconds / 60);
+    const s = Math.round(seconds % 60);
+    return `${m}m ${s}s`;
+  }
+  const h = Math.floor(seconds / 3600);
+  const m = Math.floor((seconds % 3600) / 60);
+  return `${h}h ${m}m`;
+}
+
+/**
+ * Format a duration in seconds to "Xms", "Xs", "Xm Ys", or "Xh Ym".
+ * Includes millisecond precision for durations less than 1 second.
+ */
+export function formatDuration(seconds: number | null): string {
+  if (seconds == null || seconds <= 0) return "--";
+  if (seconds < 1) return `${Math.round(seconds * 1000)}ms`;
+  if (seconds < 60) return `${seconds.toFixed(1)}s`;
+  const m = Math.floor(seconds / 60);
+  const s = Math.round(seconds % 60);
+  if (m < 60) return `${m}m ${s}s`;
+  const h = Math.floor(m / 60);
+  const rm = m % 60;
+  return `${h}h ${rm}m`;
+}

From 4db7dd4ad9ebcb5331b9536028d77aac6f8f54f9 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:30:28 -0700
Subject: [PATCH 042/173] Frontend: Add date formatters

---
 frontend/src/utils/format/date.ts | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 frontend/src/utils/format/date.ts

diff --git a/frontend/src/utils/format/date.ts b/frontend/src/utils/format/date.ts
new file mode 100644
index 0000000..c7c0635
--- /dev/null
+++ b/frontend/src/utils/format/date.ts
@@ -0,0 +1,25 @@
+/**
+ * Format a Unix timestamp (seconds) to a locale date string (date only).
+ */
+export function formatDate(mtime: number): string {
+  return new Date(mtime * 1000).toLocaleDateString(undefined, {
+    year: "numeric",
+    month: "short",
+    day: "numeric",
+  });
+}
+
+/**
+ * Format a Unix timestamp (seconds) to a locale datetime string (date + time).
+ * Returns "-" for null/undefined values.
+ */
+export function formatDateTime(epochSeconds: number | null | undefined): string {
+  if (!epochSeconds) return "-";
+  return new Date(epochSeconds * 1000).toLocaleString("en-US", {
+    month: "short",
+    day: "numeric",
+    year: "numeric",
+    hour: "2-digit",
+    minute: "2-digit",
+  });
+}

From 8aed27c31f9e547d8bdd568dbf9ff99050dc269f Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:31:16 -0700
Subject: [PATCH 043/173] Utils: Add csv download helper

---
 frontend/src/utils/csv.ts | 40 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 frontend/src/utils/csv.ts

diff --git a/frontend/src/utils/csv.ts b/frontend/src/utils/csv.ts
new file mode 100644
index 0000000..9a7948f
--- /dev/null
+++ b/frontend/src/utils/csv.ts
@@ -0,0 +1,40 @@
+/** CSV export utility for the upload summary. */
+
+import type { UnifiedFileRow } from "../types/upload.ts";
+
+/**
+ * Generate and download a CSV file from the unified file rows.
+ */
+export function downloadUploadCsv(files: UnifiedFileRow[], jobId: string): void {
+  const header = "Filename,Folder,Size,Status,S3 Path,Duration (s),Speed (Mbps),Error\n";
+  const rows = files
+    .map((f) => {
+      const cols = [
+        csvEscape(f.filename),
+        csvEscape(f.folder),
+        f.size.toString(),
+        f.status,
+        csvEscape(f.s3Path),
+        f.duration?.toFixed(2) ?? "",
+        f.speed?.toFixed(2) ?? "",
+        csvEscape(f.error),
+      ];
+      return cols.join(",");
+    })
+    .join("\n");
+
+  const blob = new Blob([header + rows], { type: "text/csv" });
+  const url = URL.createObjectURL(blob);
+  const a = document.createElement("a");
+  a.href = url;
+  a.download = `upload-summary-${jobId.slice(0, 8)}.csv`;
+  a.click();
+  URL.revokeObjectURL(url);
+}
+
+function csvEscape(value: string): string {
+  if (value.includes(",") || value.includes('"') || value.includes("\n")) {
+    return `"${value.replace(/"/g, '""')}"`;
+  }
+  return value;
+}

From aed4975125f4faa9b4b456727e31c47ddb53cf88 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:31:38 -0700
Subject: [PATCH 044/173] Frontend: Add common icons entry point

---
 frontend/src/utils/icons.tsx | 64 ++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 frontend/src/utils/icons.tsx

diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
new file mode 100644
index 0000000..be50850
--- /dev/null
+++ b/frontend/src/utils/icons.tsx
@@ -0,0 +1,64 @@
+/**
+ * Icon exports using lucide-react.
+ * Centralized icon library for consistent styling across the app.
+ */
+
+import {
+  File,
+  Folder,
+  Check,
+  ChevronRight,
+  X,
+  AlertTriangle,
+  AlertCircle,
+  Info,
+  CheckCircle,
+  ChevronUp,
+  ChevronDown,
+  Shield,
+  Upload,
+  Download,
+  Search,
+  Filter,
+  MoreVertical,
+  Trash2,
+  Settings,
+  RefreshCw,
+  XCircle,
+  type LucideProps,
+} from "lucide-react";
+
+// Re-export with consistent names
+export const FileIcon = File;
+export const FolderIcon = Folder;
+export const CheckIcon = Check;
+export const ChevronRightIcon = ChevronRight;
+export const XIcon = X;
+export const WarningIcon = AlertTriangle;
+export const ErrorIcon = AlertCircle;
+export const InfoIcon = Info;
+export const SuccessIcon = CheckCircle;
+export const ChevronUpIcon = ChevronUp;
+export const ChevronDownIcon = ChevronDown;
+export const ShieldIcon = Shield;
+export const UploadIcon = Upload;
+export const DownloadIcon = Download;
+export const SearchIcon = Search;
+export const FilterIcon = Filter;
+export const MoreIcon = MoreVertical;
+export const TrashIcon = Trash2;
+export const SettingsIcon = Settings;
+export const RefreshIcon = RefreshCw;
+export const XCircleIcon = XCircle;
+
+// Export type for icon props
+export type { LucideProps as IconProps };
+
+// Default icon size classes
+export const iconSizes = {
+  xs: "w-3 h-3",
+  sm: "w-4 h-4",
+  md: "w-5 h-5",
+  lg: "w-6 h-6",
+  xl: "w-8 h-8",
+} as const;

From f23e03b4d6dd3d89c9e9121e53db3da1e40faca6 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:32:20 -0700
Subject: [PATCH 045/173] Frontend: Add alert banner component

---
 .../src/components/common/AlertBanner.tsx     | 78 +++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 frontend/src/components/common/AlertBanner.tsx

diff --git a/frontend/src/components/common/AlertBanner.tsx b/frontend/src/components/common/AlertBanner.tsx
new file mode 100644
index 0000000..9013a4f
--- /dev/null
+++ b/frontend/src/components/common/AlertBanner.tsx
@@ -0,0 +1,78 @@
+/**
+ * Reusable alert banner for displaying information, warnings, errors, and success messages.
+ */
+
+import { InfoIcon, WarningIcon, ErrorIcon, SuccessIcon, ShieldIcon } from "../../utils/icons.tsx";
+import type { ReactNode } from "react";
+
+type AlertType = "info" | "warning" | "error" | "success" | "shield";
+
+interface AlertBannerProps {
+  type: AlertType;
+  title?: string;
+  message: ReactNode;
+  icon?: ReactNode;
+  className?: string;
+}
+
+const alertStyles: Record<AlertType, string> = {
+  info: "bg-blue-50 border-blue-200",
+  warning: "bg-yellow-50 border-yellow-200",
+  error: "bg-red-50 border-red-200",
+  success: "bg-green-50 border-green-200",
+  shield: "bg-green-50 border-green-200",
+};
+
+const titleStyles: Record<AlertType, string> = {
+  info: "text-blue-800",
+  warning: "text-yellow-800",
+  error: "text-red-800",
+  success: "text-green-800",
+  shield: "text-green-800",
+};
+
+const messageStyles: Record<AlertType, string> = {
+  info: "text-blue-700",
+  warning: "text-yellow-700",
+  error: "text-red-700",
+  success: "text-green-700",
+  shield: "text-green-700",
+};
+
+const iconMap: Record<AlertType, typeof InfoIcon> = {
+  info: InfoIcon,
+  warning: WarningIcon,
+  error: ErrorIcon,
+  success: SuccessIcon,
+  shield: ShieldIcon,
+};
+
+const iconColorStyles: Record<AlertType, string> = {
+  info: "text-blue-500",
+  warning: "text-yellow-500",
+  error: "text-red-500",
+  success: "text-green-500",
+  shield: "text-green-500",
+};
+
+export default function AlertBanner({
+  type,
+  title,
+  message,
+  icon,
+  className = "",
+}: AlertBannerProps) {
+  const Icon = iconMap[type];
+
+  return (
+    <div className={`border rounded-lg p-4 ${alertStyles[type]} ${className}`}>
+      <div className="flex items-start gap-3">
+        {icon || <Icon className={`w-6 h-6 mt-0.5 shrink-0 ${iconColorStyles[type]}`} />}
+        <div className="flex-1">
+          {title && <h3 className={`text-sm font-semibold ${titleStyles[type]}`}>{title}</h3>}
+          <div className={`text-sm ${messageStyles[type]} ${title ? "mt-1" : ""}`}>{message}</div>
+        </div>
+      </div>
+    </div>
+  );
+}

From 194268678080071e8f2a93a4776e0d265ed140d4 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:32:54 -0700
Subject: [PATCH 046/173] Frontend: Add breadcrumb component

---
 frontend/src/components/common/Breadcrumb.tsx | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 frontend/src/components/common/Breadcrumb.tsx

diff --git a/frontend/src/components/common/Breadcrumb.tsx b/frontend/src/components/common/Breadcrumb.tsx
new file mode 100644
index 0000000..9e408aa
--- /dev/null
+++ b/frontend/src/components/common/Breadcrumb.tsx
@@ -0,0 +1,50 @@
+import { useEffect, useRef } from "react";
+import { ChevronRightIcon } from "../../utils/icons.tsx";
+
+interface BreadcrumbItem {
+  label: string;
+  onClick?: () => void;
+}
+
+interface BreadcrumbProps {
+  items: BreadcrumbItem[];
+}
+
+export default function Breadcrumb({ items }: BreadcrumbProps) {
+  const scrollRef = useRef<HTMLElement>(null);
+
+  // Auto-scroll to the end so the current folder is always visible
+  useEffect(() => {
+    const el = scrollRef.current;
+    if (el) {
+      el.scrollLeft = el.scrollWidth;
+    }
+  }, [items]);
+
+  return (
+    <nav
+      ref={scrollRef}
+      className="flex items-center text-sm text-gray-500 overflow-x-auto whitespace-nowrap scrollbar-hide"
+      aria-label="Breadcrumb"
+    >
+      {items.map((item, index) => {
+        const isLast = index === items.length - 1;
+        return (
+          <span key={index} className="flex items-center flex-shrink-0">
+            {index > 0 && <ChevronRightIcon className="w-4 h-4 mx-1 text-gray-400" />}
+            {isLast || !item.onClick ? (
+              <span className={isLast ? "text-gray-900 font-medium" : ""}>{item.label}</span>
+            ) : (
+              <button
+                onClick={item.onClick}
+                className="hover:text-nlr-blue hover:underline"
+              >
+                {item.label}
+              </button>
+            )}
+          </span>
+        );
+      })}
+    </nav>
+  );
+}

From dca3fef02090c4ae5f4c74e5236c1aa25d06a8ea Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:33:10 -0700
Subject: [PATCH 047/173] Frontend: Add modal component

---
 frontend/src/components/common/Modal.tsx | 60 ++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 frontend/src/components/common/Modal.tsx

diff --git a/frontend/src/components/common/Modal.tsx b/frontend/src/components/common/Modal.tsx
new file mode 100644
index 0000000..0b7bb29
--- /dev/null
+++ b/frontend/src/components/common/Modal.tsx
@@ -0,0 +1,60 @@
+import { useEffect, useRef, type ReactNode } from "react";
+import { XIcon } from "../../utils/icons.tsx";
+
+interface ModalProps {
+  isOpen: boolean;
+  onClose: () => void;
+  title: string;
+  children: ReactNode;
+  footer?: ReactNode;
+}
+
+export default function Modal({ isOpen, onClose, title, children, footer }: ModalProps) {
+  const backdropRef = useRef<HTMLDivElement>(null);
+
+  useEffect(() => {
+    if (!isOpen) return;
+
+    function handleKeyDown(e: KeyboardEvent) {
+      if (e.key === "Escape") onClose();
+    }
+
+    document.addEventListener("keydown", handleKeyDown);
+    return () => document.removeEventListener("keydown", handleKeyDown);
+  }, [isOpen, onClose]);
+
+  if (!isOpen) return null;
+
+  function handleBackdropClick(e: React.MouseEvent) {
+    if (e.target === backdropRef.current) onClose();
+  }
+
+  return (
+    <div
+      ref={backdropRef}
+      className="fixed inset-0 bg-black/50 z-50 flex items-center justify-center animate-[fadeIn_0.15s_ease-out]"
+      onClick={handleBackdropClick}
+      data-testid="modal-backdrop"
+    >
+      <div className="bg-white rounded-lg shadow-xl max-w-sm w-full mx-4 overflow-hidden">
+        {/* Header */}
+        <div className="bg-nlr-blue text-white px-6 py-4 flex justify-between items-center">
+          <h2 className="text-lg font-semibold">{title}</h2>
+          <button
+            onClick={onClose}
+            className="text-white hover:text-gray-200"
+            aria-label="Close modal"
+          >
+            <XIcon className="w-6 h-6" />
+          </button>
+        </div>
+
+        {/* Body */}
+        <div className="px-6 py-5">{children}</div>
+
+        {/* Footer */}
+        {footer && <div className="bg-gray-50 px-6 py-3 flex justify-end">{footer}</div>}
+      </div>
+    </div>
+  );
+}

From fe13d4ee279f8b2b5ce16d3290a5ff896414ab76 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:33:43 -0700
Subject: [PATCH 048/173] Frontend: Add Notification component

---
 .../src/components/common/Notification.tsx    | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 frontend/src/components/common/Notification.tsx

diff --git a/frontend/src/components/common/Notification.tsx b/frontend/src/components/common/Notification.tsx
new file mode 100644
index 0000000..2ae1ea3
--- /dev/null
+++ b/frontend/src/components/common/Notification.tsx
@@ -0,0 +1,47 @@
+import { useAppStore, type Notification as NotificationType } from "../../stores/appStore.ts";
+import { SuccessIcon, ErrorIcon, InfoIcon, WarningIcon, XIcon } from "../../utils/icons.tsx";
+
+const typeStyles: Record<NotificationType["type"], string> = {
+  success: "bg-green-50 border-green-400 text-green-800",
+  error: "bg-red-50 border-red-400 text-red-800",
+  info: "bg-blue-50 border-blue-400 text-blue-800",
+  warning: "bg-yellow-50 border-yellow-400 text-yellow-800",
+};
+
+const iconMap: Record<NotificationType["type"], typeof InfoIcon> = {
+  success: SuccessIcon,
+  error: ErrorIcon,
+  info: InfoIcon,
+  warning: WarningIcon,
+};
+
+export default function NotificationStack() {
+  const notifications = useAppStore((s) => s.notifications);
+  const removeNotification = useAppStore((s) => s.removeNotification);
+
+  if (notifications.length === 0) return null;
+
+  return (
+    <div className="fixed top-4 right-4 z-[60] flex flex-col gap-2 max-w-sm" data-testid="notification-stack">
+      {notifications.map((n) => {
+        const Icon = iconMap[n.type];
+        return (
+          <div
+            key={n.id}
+            className={`border-l-4 rounded-r-lg p-4 shadow-lg flex items-start gap-3 animate-[fadeIn_0.2s_ease-out] ${typeStyles[n.type]}`}
+          >
+            <Icon className="w-5 h-5 flex-shrink-0 mt-0.5" />
+            <span className="text-sm flex-grow">{n.message}</span>
+            <button
+              onClick={() => removeNotification(n.id)}
+              className="flex-shrink-0 hover:opacity-70"
+              aria-label="Dismiss notification"
+            >
+              <XIcon className="w-4 h-4" />
+            </button>
+          </div>
+        );
+      })}
+    </div>
+  );
+}

From ba0d70a1d311923addc0e4131dde79c3d620b42d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:34:00 -0700
Subject: [PATCH 049/173] Frontend: Add progress bar component

---
 .../src/components/common/ProgressBar.tsx     | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 frontend/src/components/common/ProgressBar.tsx

diff --git a/frontend/src/components/common/ProgressBar.tsx b/frontend/src/components/common/ProgressBar.tsx
new file mode 100644
index 0000000..299b76c
--- /dev/null
+++ b/frontend/src/components/common/ProgressBar.tsx
@@ -0,0 +1,34 @@
+interface ProgressBarProps {
+  percent: number;
+  label?: string;
+  color?: string;
+}
+
+export default function ProgressBar({
+  percent,
+  label,
+  color = "bg-nlr-blue",
+}: ProgressBarProps) {
+  const clampedPercent = Math.min(100, Math.max(0, percent));
+
+  return (
+    <div>
+      {label && (
+        <div className="flex justify-between text-sm text-gray-600 mb-1">
+          <span>{label}</span>
+          <span>{Math.round(clampedPercent)}%</span>
+        </div>
+      )}
+      <div className="w-full bg-gray-200 rounded-full h-4 overflow-hidden">
+        <div
+          className={`progress-bar h-full rounded-full ${color}`}
+          style={{ width: `${clampedPercent}%` }}
+          role="progressbar"
+          aria-valuenow={clampedPercent}
+          aria-valuemin={0}
+          aria-valuemax={100}
+        />
+      </div>
+    </div>
+  );
+}

From 5cb15d573510d69d49cbe2fc91745aa1fe621b68 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:42:06 -0700
Subject: [PATCH 050/173] Frontend: Add spinner icon

---
 frontend/src/utils/icons.tsx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
index be50850..1ab5b52 100644
--- a/frontend/src/utils/icons.tsx
+++ b/frontend/src/utils/icons.tsx
@@ -25,6 +25,7 @@ import {
   Settings,
   RefreshCw,
   XCircle,
+  Loader2,
   type LucideProps,
 } from "lucide-react";
 
@@ -50,6 +51,7 @@ export const TrashIcon = Trash2;
 export const SettingsIcon = Settings;
 export const RefreshIcon = RefreshCw;
 export const XCircleIcon = XCircle;
+export const SpinnerIcon = Loader2;
 
 // Export type for icon props
 export type { LucideProps as IconProps };

From 8cead7f1eb644142ac74f607b3cddcf354105add Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:42:37 -0700
Subject: [PATCH 051/173] Frontend: Add spinner component

---
 frontend/src/components/common/Spinner.tsx | 25 ++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 frontend/src/components/common/Spinner.tsx

diff --git a/frontend/src/components/common/Spinner.tsx b/frontend/src/components/common/Spinner.tsx
new file mode 100644
index 0000000..67436f9
--- /dev/null
+++ b/frontend/src/components/common/Spinner.tsx
@@ -0,0 +1,25 @@
+import { SpinnerIcon } from "../../utils/icons";
+
+interface SpinnerProps {
+  message?: string;
+  size?: "sm" | "md" | "lg";
+}
+
+const sizeMap = {
+  sm: 20,
+  md: 32,
+  lg: 48,
+};
+
+export default function Spinner({ message, size = "md" }: SpinnerProps) {
+  return (
+    <div className="flex flex-col items-center gap-3">
+      <SpinnerIcon
+        className="animate-spin text-nlr-blue"
+        size={sizeMap[size]}
+        data-testid="spinner"
+      />
+      {message && <p className="text-sm text-gray-500">{message}</p>}
+    </div>
+  );
+}

From 7258d92c944e22aaa9d9de281745ce570f71d5d3 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:43:05 -0700
Subject: [PATCH 052/173] Frontend: add SortableHeader component

---
 .../src/components/common/SortableHeader.tsx  | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 frontend/src/components/common/SortableHeader.tsx

diff --git a/frontend/src/components/common/SortableHeader.tsx b/frontend/src/components/common/SortableHeader.tsx
new file mode 100644
index 0000000..0a690af
--- /dev/null
+++ b/frontend/src/components/common/SortableHeader.tsx
@@ -0,0 +1,29 @@
+import { ChevronUpIcon, ChevronDownIcon } from "../../utils/icons.tsx";
+
+interface SortableHeaderProps {
+  label: string;
+  active: boolean;
+  ascending: boolean;
+  onSort: () => void;
+}
+
+export default function SortableHeader({ label, active, ascending, onSort }: SortableHeaderProps) {
+  return (
+    <th
+      className="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:text-gray-700 select-none"
+      onClick={onSort}
+    >
+      <span className="inline-flex items-center gap-1">
+        {label}
+        <span className={`inline-flex flex-col leading-none ${active ? "text-nlr-blue" : "text-gray-300"}`}>
+          <ChevronUpIcon
+            className={`w-3 h-3 ${active && ascending ? "text-nlr-blue" : ""}`}
+          />
+          <ChevronDownIcon
+            className={`w-3 h-3 ${active && !ascending ? "text-nlr-blue" : ""}`}
+          />
+        </span>
+      </span>
+    </th>
+  );
+}

From 8327c0865403a1591423200ae476805c59d9fad0 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:43:23 -0700
Subject: [PATCH 053/173] Frontend: Add StatCard component

---
 frontend/src/components/common/StatCard.tsx | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 frontend/src/components/common/StatCard.tsx

diff --git a/frontend/src/components/common/StatCard.tsx b/frontend/src/components/common/StatCard.tsx
new file mode 100644
index 0000000..185346c
--- /dev/null
+++ b/frontend/src/components/common/StatCard.tsx
@@ -0,0 +1,14 @@
+interface StatCardProps {
+  value: string | number;
+  label: string;
+  color?: string;
+}
+
+export default function StatCard({ value, label, color = "text-nlr-blue" }: StatCardProps) {
+  return (
+    <div className="bg-white rounded-lg border border-gray-200 px-4 py-3 text-center">
+      <div className={`text-2xl font-semibold ${color}`}>{value}</div>
+      <div className="text-xs text-gray-500 uppercase tracking-wide mt-1">{label}</div>
+    </div>
+  );
+}

From fe237b18a9e910e4ac407b1643092a56c88f11dd Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:44:11 -0700
Subject: [PATCH 054/173] Frontend: Add Stepper component

---
 frontend/src/components/common/Stepper.tsx | 108 +++++++++++++++++++++
 1 file changed, 108 insertions(+)
 create mode 100644 frontend/src/components/common/Stepper.tsx

diff --git a/frontend/src/components/common/Stepper.tsx b/frontend/src/components/common/Stepper.tsx
new file mode 100644
index 0000000..7ba4754
--- /dev/null
+++ b/frontend/src/components/common/Stepper.tsx
@@ -0,0 +1,108 @@
+/**
+ * Unified step progress indicator for multi-step workflows.
+ *
+ * - Green circle + checkmark = completed step
+ * - Blue circle + number = active step
+ * - Gray circle + number = future step
+ * - Completed steps are clickable (go back) when not in active operation.
+ */
+
+import { CheckIcon } from "../../utils/icons.tsx";
+
+interface StepDef {
+  number: number;
+  label: string;
+}
+
+interface StepperProps {
+  steps: StepDef[];
+  currentStep: number;
+  onStepClick?: (step: number) => void;
+  /** When true, disables clicking back to earlier steps. */
+  isOperating?: boolean;
+  /** Maximum step number that can be clicked back to (default: 2) */
+  maxClickableStep?: number;
+  /** ARIA label for the navigation element */
+  ariaLabel?: string;
+  /** Test ID prefix for step buttons */
+  testIdPrefix?: string;
+}
+
+export default function Stepper({
+  steps,
+  currentStep,
+  onStepClick,
+  isOperating = false,
+  maxClickableStep = 2,
+  ariaLabel = "Progress steps",
+  testIdPrefix = "step",
+}: StepperProps) {
+  return (
+    <nav className="flex items-center justify-center mb-8" aria-label={ariaLabel}>
+      {steps.map((step, index) => {
+        const isDone = step.number < currentStep;
+        const isActive = step.number === currentStep;
+        const isFuture = step.number > currentStep;
+
+        // Only allow clicking completed steps up to maxClickableStep while not operating.
+        const canClick =
+          isDone && !isOperating && step.number <= maxClickableStep && !!onStepClick;
+
+        function handleClick() {
+          if (canClick) onStepClick(step.number);
+        }
+
+        // Circle styling
+        let circleClass =
+          "w-9 h-9 rounded-full flex items-center justify-center text-sm font-bold transition-colors";
+        if (isDone) {
+          circleClass += " bg-green-500 text-white";
+          if (canClick) circleClass += " cursor-pointer hover:bg-green-600";
+        } else if (isActive) {
+          circleClass += " bg-nlr-blue text-white";
+        } else {
+          circleClass += " bg-gray-300 text-gray-500";
+        }
+
+        // Connector line between steps
+        const showConnector = index < steps.length - 1;
+
+        return (
+          <div key={step.number} className="flex items-center">
+            <div className="flex flex-col items-center">
+              <button
+                type="button"
+                className={circleClass}
+                onClick={handleClick}
+                disabled={!canClick}
+                aria-current={isActive ? "step" : undefined}
+                aria-label={`Step ${step.number}: ${step.label}${isDone ? " (completed)" : ""}${isActive ? " (current)" : ""}`}
+                data-testid={`${testIdPrefix}-${step.number}`}
+              >
+                {isDone ? <CheckIcon className="w-5 h-5" /> : step.number}
+              </button>
+              <span
+                className={`mt-1.5 text-xs font-medium ${
+                  isDone
+                    ? "text-green-600"
+                    : isActive
+                      ? "text-nlr-blue"
+                      : "text-gray-400"
+                }${isFuture ? "" : ""}`}
+              >
+                {step.label}
+              </span>
+            </div>
+            {showConnector && (
+              <div
+                className={`w-16 sm:w-24 h-0.5 mx-2 mb-5 ${
+                  step.number < currentStep ? "bg-green-500" : "bg-gray-300"
+                }`}
+              />
+            )}
+          </div>
+        );
+      })}
+    </nav>
+  );
+}

From b05db5d730f6fca0a78760bb0652818135f57f32 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:45:00 -0700
Subject: [PATCH 055/173] Frontend: Add app version store

---
 frontend/src/stores/appStore.ts | 79 +++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 frontend/src/stores/appStore.ts

diff --git a/frontend/src/stores/appStore.ts b/frontend/src/stores/appStore.ts
new file mode 100644
index 0000000..1b5f965
--- /dev/null
+++ b/frontend/src/stores/appStore.ts
@@ -0,0 +1,79 @@
+import { create } from "zustand";
+import { apiGet, apiPut } from "../api/client.ts";
+import type { AppSettings, VersionInfo } from "../types/api.ts";
+
+export interface Notification {
+  id: string;
+  type: "success" | "error" | "info" | "warning";
+  message: string;
+}
+
+interface AppState {
+  // Settings
+  settings: AppSettings | null;
+  settingsLoading: boolean;
+  loadSettings: () => Promise<void>;
+  updateSettings: (updates: Partial<AppSettings>) => Promise<void>;
+
+  // Version
+  version: VersionInfo | null;
+  loadVersion: () => Promise<void>;
+
+  // Notifications
+  notifications: Notification[];
+  addNotification: (type: Notification["type"], message: string) => void;
+  removeNotification: (id: string) => void;
+}
+
+export const useAppStore = create<AppState>((set, get) => ({
+  // Settings
+  settings: null,
+  settingsLoading: false,
+
+  loadSettings: async () => {
+    set({ settingsLoading: true });
+    try {
+      const settings = await apiGet<AppSettings>("/api/settings");
+      set({ settings, settingsLoading: false });
+    } catch {
+      set({ settingsLoading: false });
+      get().addNotification("error", "Failed to load settings");
+    }
+  },
+
+  updateSettings: async (updates) => {
+    try {
+      const settings = await apiPut<AppSettings>("/api/settings", updates);
+      set({ settings });
+      get().addNotification("success", "Settings saved");
+    } catch {
+      get().addNotification("error", "Failed to save settings");
+    }
+  },
+
+  // Version
+  version: null,
+
+  loadVersion: async () => {
+    try {
+      const version = await apiGet<VersionInfo>("/api/settings/version");
+      set({ version });
+    } catch {
+      // Silently fail — version is non-critical
+    }
+  },
+
+  // Notifications
+  notifications: [],
+
+  addNotification: (type, message) => {
+    const id = crypto.randomUUID();
+    set((s) => ({ notifications: [...s.notifications, { id, type, message }] }));
+    // Auto-remove after 5 seconds
+    setTimeout(() => get().removeNotification(id), 5000);
+  },
+
+  removeNotification: (id) => {
+    set((s) => ({ notifications: s.notifications.filter((n) => n.id !== id) }));
+  },
+}));

From a99b86138def38a403be0bb06bf68878e2de0396 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:47:34 -0700
Subject: [PATCH 056/173] Frontend: Add file Store

---
 frontend/src/stores/fileStore.ts | 397 +++++++++++++++++++++++++++++++
 1 file changed, 397 insertions(+)
 create mode 100644 frontend/src/stores/fileStore.ts

diff --git a/frontend/src/stores/fileStore.ts b/frontend/src/stores/fileStore.ts
new file mode 100644
index 0000000..919ec2a
--- /dev/null
+++ b/frontend/src/stores/fileStore.ts
@@ -0,0 +1,397 @@
+/**
+ * FileStore — manages the Map<string, UnifiedFileRow> for the unified upload table.
+ *
+ * Exposes a useSyncExternalStore-compatible interface. Uses rAF batching
+ * so that multiple SSE updates within a single frame coalesce into one
+ * React re-render.
+ */
+
+import type { FileUploadState, ScannedFolder } from "../types/api.ts";
+import type {
+  SortDir,
+  SortKey,
+  StatusFilter,
+  UnifiedFileRow,
+  UnifiedStatus,
+} from "../types/upload.ts";
+
+type Listener = () => void;
+
+export class FileStore {
+  private rows = new Map<string, UnifiedFileRow>();
+  private listeners = new Set<Listener>();
+  private snapshot: UnifiedFileRow[] = [];
+  private dirty = true;
+
+  // Sort / filter state
+  private sortKey: SortKey = "filename";
+  private sortDir: SortDir = "asc";
+  private filter: StatusFilter = "all";
+  private search = "";
+
+  // Frozen sort — during upload, positions stay fixed
+  private frozen = false;
+  private frozenArray: UnifiedFileRow[] = [];
+
+  // rAF batching
+  private rafId: number | null = null;
+
+  // ── useSyncExternalStore interface ──
+
+  subscribe = (listener: Listener): (() => void) => {
+    this.listeners.add(listener);
+    return () => this.listeners.delete(listener);
+  };
+
+  getSnapshot = (): UnifiedFileRow[] => {
+    if (this.dirty) {
+      this.snapshot = this.buildSnapshot();
+      this.dirty = false;
+    }
+    return this.snapshot;
+  };
+
+  // ── Public getters ──
+
+  getRow(path: string): UnifiedFileRow | undefined {
+    return this.rows.get(path);
+  }
+
+  getAllRows(): Map<string, UnifiedFileRow> {
+    return this.rows;
+  }
+
+  getSortKey(): SortKey {
+    return this.sortKey;
+  }
+
+  getSortDir(): SortDir {
+    return this.sortDir;
+  }
+
+  getFilter(): StatusFilter {
+    return this.filter;
+  }
+
+  getSearch(): string {
+    return this.search;
+  }
+
+  getSize(): number {
+    return this.rows.size;
+  }
+
+  isFrozen(): boolean {
+    return this.frozen;
+  }
+
+  // ── Populate from scan ──
+
+  buildFromScan(folders: ScannedFolder[]): void {
+    this.rows.clear();
+    for (const folder of folders) {
+      this.addFolderInternal(folder);
+    }
+    this.invalidate();
+    this.notify();
+  }
+
+  addFolderFromScan(folder: ScannedFolder): void {
+    this.addFolderInternal(folder);
+    this.invalidate();
+    this.notify();
+  }
+
+  private addFolderInternal(folder: ScannedFolder): void {
+    for (const file of folder.files) {
+      if (this.rows.has(file.path)) continue;
+      const uploaded = file.already_uploaded ?? false;
+      this.rows.set(file.path, {
+        path: file.path,
+        filename: file.filename,
+        size: file.size,
+        folder: folder.relative_path === "." ? "" : folder.relative_path,
+        mtime: file.mtime,
+        alreadyUploaded: uploaded,
+        status: uploaded ? "already_uploaded" : "new",
+        progressPercent: 0,
+        s3Path: "",
+        duration: null,
+        speed: null,
+        error: "",
+      });
+    }
+  }
+
+  // ── Per-file update (called from SSE callbacks) ──
+
+  updateFile(path: string, update: Partial<UnifiedFileRow>): void {
+    const existing = this.rows.get(path);
+    if (!existing) return;
+
+    // Shallow-clone so React.memo detects a new reference
+    const updated = { ...existing, ...update };
+    this.rows.set(path, updated);
+
+    // If frozen, update the frozen array in-place at O(1)
+    if (this.frozen && updated._frozenIndex != null) {
+      this.frozenArray[updated._frozenIndex] = updated;
+    }
+
+    this.invalidate();
+    this.scheduleNotify();
+  }
+
+  // ── Bulk merge from terminal UploadJob ──
+
+  mergeCompletion(files: FileUploadState[]): void {
+    for (const f of files) {
+      const existing = this.rows.get(f.local_path);
+      if (!existing) continue;
+
+      this.rows.set(f.local_path, {
+        ...existing,
+        status: mapApiStatus(f.status),
+        progressPercent: f.progress_percent,
+        s3Path: f.s3_path,
+        duration: f.upload_duration_seconds,
+        speed: f.upload_speed_mbps,
+        error: f.error_message,
+      });
+    }
+    this.invalidate();
+    this.notify();
+  }
+
+  // ── Transition: review → upload ──
+
+  markSelectedAsPending(paths: Set<string>): void {
+    // Remove unselected rows, keep only selected
+    for (const [key] of this.rows) {
+      if (!paths.has(key)) {
+        this.rows.delete(key);
+      }
+    }
+    // All remaining rows are "queued"
+    for (const [key, row] of this.rows) {
+      this.rows.set(key, { ...row, status: "queued" });
+    }
+    this.invalidate();
+    this.notify();
+  }
+
+  // ── Freeze / unfreeze sort ──
+
+  freezeSort(): void {
+    // Build the frozen array from the current snapshot and stamp indices
+    const current = this.buildSnapshot();
+    this.frozenArray = [...current];
+    for (let i = 0; i < this.frozenArray.length; i++) {
+      const row = this.frozenArray[i]!;
+      const updated = { ...row, _frozenIndex: i };
+      this.frozenArray[i] = updated;
+      this.rows.set(row.path, updated);
+    }
+    this.frozen = true;
+    this.invalidate();
+    this.notify();
+  }
+
+  unfreezeSort(): void {
+    this.frozen = false;
+    this.frozenArray = [];
+    // Clear frozen indices
+    for (const [key, row] of this.rows) {
+      if (row._frozenIndex != null) {
+        this.rows.set(key, { ...row, _frozenIndex: undefined });
+      }
+    }
+    this.invalidate();
+    this.notify();
+  }
+
+  // ── Sort / filter / search ──
+
+  setSort(key: SortKey, dir?: SortDir): void {
+    if (dir) {
+      this.sortKey = key;
+      this.sortDir = dir;
+    } else if (this.sortKey === key) {
+      this.sortDir = this.sortDir === "asc" ? "desc" : "asc";
+    } else {
+      this.sortKey = key;
+      this.sortDir = "asc";
+    }
+    // Re-freeze with new sort if frozen
+    if (this.frozen) {
+      this.frozen = false; // temporarily unfreeze to rebuild
+      this.freezeSort();
+      return;
+    }
+    this.invalidate();
+    this.notify();
+  }
+
+  setFilter(filter: StatusFilter): void {
+    this.filter = filter;
+    this.invalidate();
+    this.notify();
+  }
+
+  setSearch(query: string): void {
+    this.search = query;
+    this.invalidate();
+    this.notify();
+  }
+
+  // ── Reset ──
+
+  clear(): void {
+    this.rows.clear();
+    this.snapshot = [];
+    this.dirty = false;
+    this.frozen = false;
+    this.frozenArray = [];
+    this.sortKey = "filename";
+    this.sortDir = "asc";
+    this.filter = "all";
+    this.search = "";
+    if (this.rafId != null) {
+      cancelAnimationFrame(this.rafId);
+      this.rafId = null;
+    }
+    this.notify();
+  }
+
+  // ── Internals ──
+
+  private buildSnapshot(): UnifiedFileRow[] {
+    const source = this.frozen ? this.frozenArray : Array.from(this.rows.values());
+    let result = source;
+
+    // Filter
+    result = this.applyFilter(result);
+
+    // Search
+    if (this.search) {
+      const q = this.search.toLowerCase();
+      result = result.filter(
+        (r) =>
+          r.filename.toLowerCase().includes(q) ||
+          r.folder.toLowerCase().includes(q),
+      );
+    }
+
+    // Sort (skip if frozen — positions are fixed)
+    if (!this.frozen) {
+      result = this.applySort(result);
+    }
+
+    return result;
+  }
+
+  private applyFilter(rows: UnifiedFileRow[]): UnifiedFileRow[] {
+    switch (this.filter) {
+      case "all":
+        return rows;
+      case "new":
+        return rows.filter((r) => r.status === "new" || !r.alreadyUploaded);
+      case "uploaded":
+        return rows.filter((r) => r.status === "already_uploaded" || r.alreadyUploaded);
+      case "queued":
+        return rows.filter((r) => r.status === "queued");
+      case "in_progress":
+        return rows.filter((r) => r.status === "in_progress");
+      case "completed":
+        return rows.filter((r) => r.status === "completed");
+      case "skipped":
+        return rows.filter((r) => r.status === "skipped");
+      case "failed":
+        return rows.filter((r) => r.status === "failed");
+      default:
+        return rows;
+    }
+  }
+
+  private applySort(rows: UnifiedFileRow[]): UnifiedFileRow[] {
+    const dir = this.sortDir === "asc" ? 1 : -1;
+    return [...rows].sort((a, b) => {
+      switch (this.sortKey) {
+        case "filename":
+          return dir * a.filename.localeCompare(b.filename);
+        case "folder":
+          return dir * a.folder.localeCompare(b.folder);
+        case "size":
+          return dir * (a.size - b.size);
+        case "mtime":
+          return dir * (a.mtime - b.mtime);
+        case "status": {
+          return dir * (statusOrder(a.status) - statusOrder(b.status));
+        }
+        default:
+          return 0;
+      }
+    });
+  }
+
+  private invalidate(): void {
+    this.dirty = true;
+  }
+
+  private notify(): void {
+    for (const listener of this.listeners) {
+      listener();
+    }
+  }
+
+  private scheduleNotify(): void {
+    if (this.rafId != null) return;
+    this.rafId = requestAnimationFrame(() => {
+      this.rafId = null;
+      this.notify();
+    });
+  }
+}
+
+// ── Helpers ──
+
+function mapApiStatus(status: string): UnifiedStatus {
+  switch (status) {
+    case "completed":
+      return "completed";
+    case "skipped":
+      return "skipped";
+    case "failed":
+    case "cancelled":
+      return "failed";
+    case "uploading":
+    case "analyzing":
+      return "in_progress";
+    default:
+      return "queued";
+  }
+}
+
+function statusOrder(status: UnifiedStatus): number {
+  switch (status) {
+    case "new":
+      return 0;
+    case "already_uploaded":
+      return 1;
+    case "in_progress":
+      return 2;
+    case "queued":
+      return 3;
+    case "completed":
+      return 4;
+    case "skipped":
+      return 5;
+    case "failed":
+      return 6;
+    default:
+      return 7;
+  }
+}
+
+/** Singleton instance */
+export const fileStore = new FileStore();

From 43a4e20b69e871ef1d0001fda6073e58a5630a4d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:50:16 -0700
Subject: [PATCH 057/173] Frontend: Add upload state store

---
 frontend/src/stores/uploadStore.ts | 70 ++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 frontend/src/stores/uploadStore.ts

diff --git a/frontend/src/stores/uploadStore.ts b/frontend/src/stores/uploadStore.ts
new file mode 100644
index 0000000..5efb416
--- /dev/null
+++ b/frontend/src/stores/uploadStore.ts
@@ -0,0 +1,70 @@
+import { create } from "zustand";
+import type { ScannedFolder, UploadJob } from "../types/api.ts";
+
+export type UploadStep = 1 | 2 | 3 | 4;
+
+interface UploadState {
+  // Current step
+  step: UploadStep;
+  setStep: (step: UploadStep) => void;
+
+  // Selected folder
+  folderPath: string;
+  setFolderPath: (path: string) => void;
+
+  // Scan results
+  scanJobId: string | null;
+  scanFolders: ScannedFolder[];
+  scanComplete: boolean;
+  isScanning: boolean;
+  scanTotals: {
+    totalFiles: number;
+    alreadyUploaded: number;
+    totalSize: number;
+  };
+  setScanJobId: (id: string | null) => void;
+  addScanFolder: (folder: ScannedFolder) => void;
+  setScanComplete: (complete: boolean) => void;
+  setIsScanning: (scanning: boolean) => void;
+  updateScanTotals: (totals: { totalFiles: number; alreadyUploaded: number; totalSize: number }) => void;
+
+  // Upload job
+  uploadJobId: string | null;
+  completedJob: UploadJob | null;
+  setUploadJobId: (id: string | null) => void;
+  setCompletedJob: (job: UploadJob | null) => void;
+
+  // Reset
+  reset: () => void;
+}
+
+const initialState = {
+  step: 1 as UploadStep,
+  folderPath: "",
+  scanJobId: null,
+  scanFolders: [],
+  scanComplete: false,
+  isScanning: false,
+  scanTotals: { totalFiles: 0, alreadyUploaded: 0, totalSize: 0 },
+  uploadJobId: null,
+  completedJob: null,
+};
+
+export const useUploadStore = create<UploadState>((set) => ({
+  ...initialState,
+
+  setStep: (step) => set({ step }),
+  setFolderPath: (folderPath) => set({ folderPath }),
+
+  setScanJobId: (scanJobId) => set({ scanJobId }),
+  addScanFolder: (folder) =>
+    set((s) => ({ scanFolders: [...s.scanFolders, folder] })),
+  setScanComplete: (scanComplete) => set({ scanComplete }),
+  setIsScanning: (isScanning) => set({ isScanning }),
+  updateScanTotals: (scanTotals) => set({ scanTotals }),
+
+  setUploadJobId: (uploadJobId) => set({ uploadJobId }),
+  setCompletedJob: (completedJob) => set({ completedJob }),
+
+  reset: () => set(initialState),
+}));

From c9114a902dde71279a54b2396ca2ed2bb9f87df6 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:50:57 -0700
Subject: [PATCH 058/173] Frontend: Add delete state store

---
 frontend/src/stores/deleteStore.ts | 60 ++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 frontend/src/stores/deleteStore.ts

diff --git a/frontend/src/stores/deleteStore.ts b/frontend/src/stores/deleteStore.ts
new file mode 100644
index 0000000..44c1bfa
--- /dev/null
+++ b/frontend/src/stores/deleteStore.ts
@@ -0,0 +1,60 @@
+import { create } from "zustand";
+import type { DeleteJobResult, DeleteScanFile } from "../types/delete.ts";
+
+export type DeleteStep = 1 | 2 | 3 | 4 | 5;
+
+interface DeleteState {
+  // Current step
+  step: DeleteStep;
+  setStep: (step: DeleteStep) => void;
+
+  // Selected folder
+  folderPath: string;
+  setFolderPath: (path: string) => void;
+
+  // Scan results
+  scanResults: DeleteScanFile[];
+  scanTotalSize: number;
+  isScanning: boolean;
+  setScanResults: (files: DeleteScanFile[], totalSize: number) => void;
+  setIsScanning: (scanning: boolean) => void;
+
+  // Delete job
+  deleteJobId: string | null;
+  completedJob: DeleteJobResult | null;
+  isDeleting: boolean;
+  setDeleteJobId: (id: string | null) => void;
+  setCompletedJob: (job: DeleteJobResult | null) => void;
+  setIsDeleting: (deleting: boolean) => void;
+
+  // Reset
+  reset: () => void;
+}
+
+const initialState = {
+  step: 1 as DeleteStep,
+  folderPath: "",
+  scanResults: [] as DeleteScanFile[],
+  scanTotalSize: 0,
+  isScanning: false,
+  deleteJobId: null,
+  completedJob: null,
+  isDeleting: false,
+};
+
+export const useDeleteStore = create<DeleteState>((set) => ({
+  ...initialState,
+
+  setStep: (step) => set({ step }),
+  setFolderPath: (folderPath) => set({ folderPath }),
+
+  setScanResults: (scanResults, scanTotalSize) =>
+    set({ scanResults, scanTotalSize }),
+  setIsScanning: (isScanning) => set({ isScanning }),
+
+  setDeleteJobId: (deleteJobId) => set({ deleteJobId }),
+  setCompletedJob: (completedJob) => set({ completedJob }),
+  setIsDeleting: (isDeleting) => set({ isDeleting }),
+
+  reset: () => set(initialState),
+}));

From 4fbde71968380c3a6baf4c6e1dde03f63a5fa96d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:51:53 -0700
Subject: [PATCH 059/173] Frontend: Define types for API data passing

---
 frontend/src/types/api.ts | 395 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 395 insertions(+)
 create mode 100644 frontend/src/types/api.ts

diff --git a/frontend/src/types/api.ts b/frontend/src/types/api.ts
new file mode 100644
index 0000000..fbc3c03
--- /dev/null
+++ b/frontend/src/types/api.ts
@@ -0,0 +1,395 @@
+/** TypeScript types matching the Flask API response shapes. */
+
+// ── Upload types ──
+
+export type UploadStatus =
+  | "pending"
+  | "analyzing"
+  | "ready"
+  | "uploading"
+  | "completed"
+  | "failed"
+  | "skipped"
+  | "cancelled";
+
+export interface FileUploadState {
+  filename: string;
+  local_path: string;
+  file_size: number;
+  file_size_formatted: string;
+  status: UploadStatus;
+  s3_path: string;
+  start_time: string | null;
+  bytes_uploaded: number;
+  progress_percent: number;
+  error_message: string;
+  is_duplicate: boolean;
+  is_valid: boolean;
+  upload_started_at: string | null;
+  upload_completed_at: string | null;
+  upload_duration_seconds: number | null;
+  upload_speed_mbps: number | null;
+}
+
+export interface UploadJobProgress {
+  job_id: string;
+  status: UploadStatus;
+  progress_percent: number;
+  files_completed: number;
+  total_files: number;
+  uploaded_bytes_formatted: string;
+  total_bytes_formatted: string;
+  eta_seconds: number | null;
+  files_failed: number;
+  files_skipped: number;
+  files_uploaded: number;
+  cancelled: boolean;
+  files: FileUploadState[];
+}
+
+export interface UploadJob {
+  job_id: string;
+  status: UploadStatus;
+  files: FileUploadState[];
+  total_files: number;
+  files_completed: number;
+  files_failed: number;
+  files_skipped: number;
+  files_uploaded: number;
+  total_bytes: number;
+  total_bytes_formatted: string;
+  uploaded_bytes: number;
+  uploaded_bytes_formatted: string;
+  successfully_uploaded_bytes: number;
+  successfully_uploaded_bytes_formatted: string;
+  progress_percent: number;
+  eta_seconds: number | null;
+  created_at: string;
+  started_at: string | null;
+  completed_at: string | null;
+  total_upload_duration_seconds: number | null;
+  total_upload_duration_formatted: string | null;
+  average_upload_speed_mbps: number | null;
+  cancelled: boolean;
+  auto_upload: boolean;
+  has_valid_uploadable_files: boolean;
+  pre_filter_stats: PreFilterStats;
+}
+
+export interface PreFilterStats {
+  total: number;
+  cache_hits: number;
+  cache_skipped: number;
+  s3_hits: number;
+  no_timestamp: number;
+  to_analyze: number;
+  file_statuses?: FilePreFilterStatus[];
+}
+
+export interface FilePreFilterStatus {
+  path: string;
+  filename: string;
+  size: number;
+  mtime: number;
+  already_uploaded: boolean;
+  s3_path?: string;
+}
+
+// ── SSE event types ──
+
+export interface AnalysisProgressEvent {
+  type: "analysis_progress";
+  job_id: string;
+  job_status: UploadStatus;
+  file: FileUploadState;
+  total_files: number;
+  analysis_complete: boolean;
+}
+
+export interface AnalysisCompleteEvent {
+  type: "analysis_complete";
+  job: UploadJob;
+  auto_upload?: boolean;
+}
+
+export interface AutoUploadStartingEvent {
+  type: "auto_upload_starting";
+  job_id: string;
+}
+
+// ── Scan types ──
+
+export interface ScannedFileInfo {
+  path: string;
+  filename: string;
+  size: number;
+  mtime: number;
+  relative_path: string;
+  already_uploaded?: boolean;
+}
+
+export interface ScannedFolder {
+  relative_path: string;
+  files: ScannedFileInfo[];
+  total_files: number;
+  already_uploaded: number;
+  all_uploaded: boolean;
+  error: string | null;
+}
+
+export interface ScanStartedEvent {
+  type: "scan_started";
+  folders_total: number;
+  root_folder: string;
+}
+
+export interface ScanFolderCompleteEvent {
+  type: "scan_folder_complete";
+  folder: ScannedFolder;
+  folders_scanned: number;
+  folders_total: number;
+  running_totals: {
+    total_files_found: number;
+    total_already_uploaded: number;
+    total_size: number;
+  };
+}
+
+export interface ScanCompleteEvent {
+  type: "scan_complete";
+  status: string;
+  folders_scanned: number;
+  folders_total: number;
+  total_files_found: number;
+  total_already_uploaded: number;
+  total_size: number;
+  error?: string;
+}
+
+export type ScanEvent = ScanStartedEvent | ScanFolderCompleteEvent | ScanCompleteEvent;
+
+// ── Bulk analyze response ──
+
+export interface BulkAnalyzeResponse {
+  job_id: string;
+  status: string;
+  total_files: number;
+  pre_filter_stats: PreFilterStats;
+  auto_upload: boolean;
+}
+
+// ── File browser types ──
+
+export interface BrowseResponse {
+  success: boolean;
+  current_path: string;
+  parent_path: string | null;
+  breadcrumbs: BreadcrumbItem[];
+  quick_links: QuickLink[];
+  folders: LocalFolder[];
+  files: LocalFile[];
+  mcap_count: number;
+  total_mcap_count: number;
+  already_uploaded: number;
+}
+
+export interface BreadcrumbItem {
+  name: string;
+  path: string;
+}
+
+export interface QuickLink {
+  name: string;
+  path: string;
+}
+
+export interface LocalFolder {
+  name: string;
+  path: string;
+  mcap_count: number;
+  already_uploaded: number;
+}
+
+export interface LocalFile {
+  name: string;
+  path: string;
+  size: number;
+  mtime: number;
+  already_uploaded?: boolean;
+}
+
+// ── S3 browser types ──
+
+export interface S3ListResponse {
+  success: boolean;
+  folders: S3Folder[];
+  files: S3File[];
+  breadcrumbs: S3Breadcrumb[];
+  prefix?: string;
+  error?: string;
+}
+
+export interface S3Folder {
+  name: string;
+  prefix: string;
+}
+
+export interface S3File {
+  name: string;
+  key: string;
+  size: number;
+  last_modified: string;
+}
+
+export interface S3Breadcrumb {
+  name: string;
+  prefix: string;
+}
+
+export interface S3SearchResponse {
+  success: boolean;
+  query: string;
+  prefix: string;
+  files: S3File[];
+  total_matches: number;
+}
+
+// ── Settings types ──
+
+export interface AppSettings {
+  aws_profile: string;
+  aws_region: string;
+  s3_bucket: string;
+  default_upload_folder: string;
+  display_name: string;
+  log_directory: string;
+}
+
+export interface VersionInfo {
+  version: string;
+  commit: string;
+  branch: string;
+  dirty: boolean;
+}
+
+export interface UpdateCheckResult {
+  updates_available: boolean;
+  current_commit: string;
+  remote_commit: string;
+  commits_behind: number;
+}
+
+export interface UpdateResult {
+  success: boolean;
+  results: {
+    git_pull: { success: boolean; output: string };
+    pip_install: { success: boolean; output: string };
+    modaq_toolkit: { success: boolean; output: string };
+  };
+  message: string;
+}
+
+export interface ConnectionTestResult {
+  success: boolean;
+  message?: string;
+  error?: string;
+}
+
+export interface CacheStats {
+  success: boolean;
+  stats: {
+    total_entries: number;
+    exists_count: number;
+    not_exists_count: number;
+    bucket: string;
+  };
+}
+
+export interface CacheSyncResult {
+  success: boolean;
+  bucket?: string;
+  files_in_s3?: number;
+  files_updated?: number;
+  files_removed?: number;
+  message?: string;
+  error?: string;
+}
+
+// ── Log types ──
+
+export interface LogEntry {
+  id: number;
+  timestamp: string;
+  level: string;
+  category: string;
+  event: string;
+  message: string;
+  metadata: Record<string, unknown>;
+}
+
+export interface LogEntriesResponse {
+  entries: LogEntry[];
+  total: number;
+  offset: number;
+  limit: number;
+}
+
+export interface LogStats {
+  total_entries: number;
+  today_entries: number;
+  total_size_bytes: number;
+  level_counts: Record<string, number>;
+  category_counts: Record<string, number>;
+  date_range: { earliest: string | null; latest: string | null };
+  file_count: number;
+  csv_count: number;
+  csv_files: CsvFileInfo[];
+}
+
+export interface CsvFileInfo {
+  path: string;
+  filename: string;
+  date: string;
+  size: number;
+}
+
+export interface CsvPreviewResponse {
+  columns: string[];
+  rows: Record<string, string>[];
+}
+
+// ── Upload stats types ──
+
+export interface UploadSessionFile {
+  filename: string;
+  file_size_formatted: string;
+  status: string;
+  upload_speed_mbps: string;
+  s3_path: string;
+  error_message: string;
+}
+
+export interface UploadSession {
+  csv_path: string;
+  date: string;
+  time: string;
+  total_files: number;
+  completed: number;
+  failed: number;
+  skipped: number;
+  total_bytes: number;
+  total_bytes_formatted: string;
+  total_duration_seconds: number;
+  avg_speed_mbps: number;
+  files: UploadSessionFile[];
+}
+
+export interface UploadStatsResponse {
+  total_files_uploaded: number;
+  total_files_failed: number;
+  total_files_skipped: number;
+  total_bytes_uploaded: number;
+  total_bytes_uploaded_formatted: string;
+  total_sessions: number;
+  sessions: UploadSession[];
+}

From d6ee4cdf768597808658a068894d476c4a92ef7f Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:52:19 -0700
Subject: [PATCH 060/173] Frontend: Add types for delete state passing with
 backend

---
 frontend/src/types/delete.ts | 83 ++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 frontend/src/types/delete.ts

diff --git a/frontend/src/types/delete.ts b/frontend/src/types/delete.ts
new file mode 100644
index 0000000..0547bcf
--- /dev/null
+++ b/frontend/src/types/delete.ts
@@ -0,0 +1,83 @@
+/** TypeScript types for the Local Delete feature. */
+
+// ── File status ──
+
+export type DeleteFileStatus =
+  | "pending"
+  | "scanning"
+  | "verifying"
+  | "verified"
+  | "deleting"
+  | "deleted"
+  | "mismatch"
+  | "failed"
+  | "cancelled";
+
+// ── Scan response ──
+
+export interface DeleteScanFile {
+  filename: string;
+  local_path: string;
+  file_size: number;
+  s3_path: string;
+  s3_bucket: string;
+  status: DeleteFileStatus;
+  local_md5: string;
+  s3_etag: string;
+  s3_size: number;
+  verification: string;
+  error_message: string;
+}
+
+export interface DeleteScanResponse {
+  success: boolean;
+  job_id: string;
+  folder_path: string;
+  files: DeleteScanFile[];
+  total_files: number;
+  total_size: number;
+}
+
+// ── SSE event types ──
+
+export interface DeleteProgressEvent {
+  type: "delete_progress";
+  job_id: string;
+  status: string;
+  total_files: number;
+  files_processed: number;
+  status_counts: Record<string, number>;
+  total_deleted_size: number;
+  cancelled: boolean;
+}
+
+export interface DeleteCompleteEvent {
+  type: "delete_complete";
+  job_id: string;
+  status: string;
+  total_files: number;
+  files: DeleteScanFile[];
+  status_counts: Record<string, number>;
+  total_deleted_size: number;
+  created_at: string;
+  started_at: string | null;
+  completed_at: string | null;
+  cancelled: boolean;
+}
+
+export type DeleteSSEEvent = DeleteProgressEvent | DeleteCompleteEvent;
+
+// ── Job result (full response) ──
+
+export interface DeleteJobResult {
+  job_id: string;
+  status: string;
+  total_files: number;
+  files: DeleteScanFile[];
+  status_counts: Record<string, number>;
+  total_deleted_size: number;
+  created_at: string;
+  started_at: string | null;
+  completed_at: string | null;
+  cancelled: boolean;
+}

From 4702472d29355c61f4c270a5f4dd5dabd518a518 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:52:52 -0700
Subject: [PATCH 061/173] Frontend: Add types for upload state passing

---
 frontend/src/types/upload.ts | 49 ++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 frontend/src/types/upload.ts

diff --git a/frontend/src/types/upload.ts b/frontend/src/types/upload.ts
new file mode 100644
index 0000000..d2c8fad
--- /dev/null
+++ b/frontend/src/types/upload.ts
@@ -0,0 +1,49 @@
+/**
+ * Types for the unified upload table that persists from Step 2 through Step 4.
+ */
+
+export type UnifiedStatus =
+  | "new"
+  | "already_uploaded"
+  | "queued"
+  | "in_progress"
+  | "completed"
+  | "skipped"
+  | "failed";
+export type UploadPhase = "review" | "uploading" | "summary";
+export type SortKey = "filename" | "folder" | "size" | "mtime" | "status";
+export type SortDir = "asc" | "desc";
+export type StatusFilter =
+  | "all"
+  | "new"
+  | "uploaded"
+  | "queued"
+  | "in_progress"
+  | "completed"
+  | "skipped"
+  | "failed";
+
+export interface UnifiedFileRow {
+  /** Stable key — the local filesystem path. */
+  path: string;
+  filename: string;
+  size: number;
+  folder: string;
+  mtime: number;
+  /** Whether the file was already on S3 when scanned. */
+  alreadyUploaded: boolean;
+  /** Upload lifecycle status. */
+  status: UnifiedStatus;
+  /** 0–100 during upload. */
+  progressPercent: number;
+  /** Populated after successful upload. */
+  s3Path: string;
+  /** Upload duration in seconds. */
+  duration: number | null;
+  /** Upload speed in Mbps. */
+  speed: number | null;
+  /** Error message if failed. */
+  error: string;
+  /** Position in the frozen sort array (set during upload phase). */
+  _frozenIndex?: number;
+}

From 6347bb3b3bdd6b27aa7ab609c1809fb498c64244 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:53:36 -0700
Subject: [PATCH 062/173] Frontend: Add common debounce hook

---
 frontend/src/hooks/useDebounce.ts | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 frontend/src/hooks/useDebounce.ts

diff --git a/frontend/src/hooks/useDebounce.ts b/frontend/src/hooks/useDebounce.ts
new file mode 100644
index 0000000..2f1985f
--- /dev/null
+++ b/frontend/src/hooks/useDebounce.ts
@@ -0,0 +1,12 @@
+import { useEffect, useState } from "react";
+
+export function useDebounce<T>(value: T, delay = 300): T {
+  const [debounced, setDebounced] = useState(value);
+
+  useEffect(() => {
+    const timer = setTimeout(() => setDebounced(value), delay);
+    return () => clearTimeout(timer);
+  }, [value, delay]);
+
+  return debounced;
+}

From f7ed73ad98c482a4c7fe48c7f458a1f7f05c2f95 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:54:28 -0700
Subject: [PATCH 063/173] Frontend: Add folderScan hook

---
 frontend/src/hooks/useFolderScan.ts | 155 ++++++++++++++++++++++++++++
 1 file changed, 155 insertions(+)
 create mode 100644 frontend/src/hooks/useFolderScan.ts

diff --git a/frontend/src/hooks/useFolderScan.ts b/frontend/src/hooks/useFolderScan.ts
new file mode 100644
index 0000000..2308003
--- /dev/null
+++ b/frontend/src/hooks/useFolderScan.ts
@@ -0,0 +1,155 @@
+/**
+ * Hook that wraps the scan-folder-async API + SSE progress stream.
+ *
+ * Starts a scan via POST, then listens on the SSE progress endpoint.
+ * Updates uploadStore with scan results as they arrive.
+ */
+
+import { useCallback, useMemo, useState } from "react";
+
+import { apiPost } from "../api/client.ts";
+import { useUploadStore } from "../stores/uploadStore.ts";
+import type {
+  ScannedFolder,
+  ScanEvent,
+  ScanFolderCompleteEvent,
+  ScanCompleteEvent,
+} from "../types/api.ts";
+import { useSSE } from "./useSSE.ts";
+
+interface ScanTotals {
+  totalFiles: number;
+  alreadyUploaded: number;
+  totalSize: number;
+}
+
+interface ScanExclusions {
+  subfolders: string[];
+  files: string[];
+}
+
+interface UseFolderScanResult {
+  startScan: (folderPath: string, cacheOnly?: boolean, exclusions?: ScanExclusions) => Promise<void>;
+  cancelScan: () => Promise<void>;
+  folders: ScannedFolder[];
+  isScanning: boolean;
+  scanComplete: boolean;
+  totals: ScanTotals;
+}
+
+export function useFolderScan(): UseFolderScanResult {
+  const [jobId, setJobId] = useState<string | null>(null);
+
+  const {
+    scanFolders: folders,
+    isScanning,
+    scanComplete,
+    scanTotals: totals,
+    setScanJobId,
+    addScanFolder,
+    setScanComplete,
+    setIsScanning,
+    updateScanTotals,
+  } = useUploadStore();
+
+  /** Handle each SSE event from the scan stream. */
+  const handleMessage = useCallback(
+    (raw: unknown) => {
+      const data = raw as ScanEvent & Record<string, unknown>;
+      if (!data || typeof data !== "object") return;
+
+      switch (data.type) {
+        case "scan_started":
+          // Just update scanning state — we already set it in startScan.
+          break;
+
+        case "scan_folder_complete": {
+          const evt = data as ScanFolderCompleteEvent;
+          addScanFolder(evt.folder);
+          updateScanTotals({
+            totalFiles: evt.running_totals.total_files_found,
+            alreadyUploaded: evt.running_totals.total_already_uploaded,
+            totalSize: evt.running_totals.total_size,
+          });
+          break;
+        }
+
+        case "scan_complete": {
+          const evt = data as ScanCompleteEvent;
+          updateScanTotals({
+            totalFiles: evt.total_files_found,
+            alreadyUploaded: evt.total_already_uploaded,
+            totalSize: evt.total_size,
+          });
+          setScanComplete(true);
+          setIsScanning(false);
+          setJobId(null);
+          break;
+        }
+      }
+    },
+    [addScanFolder, updateScanTotals, setScanComplete, setIsScanning],
+  );
+
+  // Only connect when we have a jobId and are still scanning.
+  const sseUrl = useMemo(
+    () => (jobId && isScanning ? `/api/upload/progress/${jobId}` : null),
+    [jobId, isScanning],
+  );
+
+  useSSE({
+    url: sseUrl,
+    onMessage: handleMessage,
+    onError: () => {
+      // Stream ended or errored — mark complete if not already.
+      if (isScanning) {
+        setScanComplete(true);
+        setIsScanning(false);
+        setJobId(null);
+      }
+    },
+  });
+
+  /** Kick off a new folder scan. */
+  const startScan = useCallback(
+    async (folderPath: string, cacheOnly = false, exclusions?: ScanExclusions) => {
+      setIsScanning(true);
+      setScanComplete(false);
+
+      try {
+        const body: Record<string, unknown> = {
+          folder_path: folderPath,
+          cache_only: cacheOnly,
+        };
+        if (exclusions) {
+          body.excluded_subfolders = exclusions.subfolders;
+          body.excluded_files = exclusions.files;
+        }
+        const res = await apiPost<{ job_id: string }>("/api/upload/scan-folder-async", body);
+        setScanJobId(res.job_id);
+        setJobId(res.job_id);
+      } catch {
+        setIsScanning(false);
+        setScanComplete(false);
+      }
+    },
+    [setScanJobId, setIsScanning, setScanComplete],
+  );
+
+  /** Cancel an in-progress scan. */
+  const cancelScan = useCallback(async () => {
+    const currentJobId = useUploadStore.getState().scanJobId;
+    if (currentJobId) {
+      try {
+        await apiPost(`/api/upload/cancel/${currentJobId}`);
+      } catch {
+        // Ignore — may already be done.
+      }
+    }
+    setIsScanning(false);
+    setScanComplete(false);
+    setJobId(null);
+  }, [setIsScanning, setScanComplete]);
+
+  return { startScan, cancelScan, folders, isScanning, scanComplete, totals };
+}

From dafe76acafc8518b35c4af1925e05ded26a51819 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:54:55 -0700
Subject: [PATCH 064/173] Frontend: Add sorting hook

---
 frontend/src/hooks/useSorting.ts | 48 ++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 frontend/src/hooks/useSorting.ts

diff --git a/frontend/src/hooks/useSorting.ts b/frontend/src/hooks/useSorting.ts
new file mode 100644
index 0000000..35d60f0
--- /dev/null
+++ b/frontend/src/hooks/useSorting.ts
@@ -0,0 +1,48 @@
+import { useCallback, useMemo, useState } from "react";
+
+export interface UseSortingResult<T extends string> {
+  sortColumn: T;
+  ascending: boolean;
+  toggleSort: (column: T) => void;
+  sortFn: <R extends Record<string, unknown>>(a: R, b: R) => number;
+}
+
+export function useSorting<T extends string>(
+  defaultColumn: T,
+  defaultAscending = true,
+): UseSortingResult<T> {
+  const [sortColumn, setSortColumn] = useState<T>(defaultColumn);
+  const [ascending, setAscending] = useState(defaultAscending);
+
+  const toggleSort = useCallback(
+    (column: T) => {
+      if (column === sortColumn) {
+        setAscending((prev) => !prev);
+      } else {
+        setSortColumn(column);
+        setAscending(true);
+      }
+    },
+    [sortColumn],
+  );
+
+  const sortFn = useMemo(() => {
+    return <R extends Record<string, unknown>>(a: R, b: R): number => {
+      const aVal = a[sortColumn];
+      const bVal = b[sortColumn];
+
+      let comparison = 0;
+      if (typeof aVal === "string" && typeof bVal === "string") {
+        comparison = aVal.localeCompare(bVal);
+      } else if (typeof aVal === "number" && typeof bVal === "number") {
+        comparison = aVal - bVal;
+      } else {
+        comparison = String(aVal ?? "").localeCompare(String(bVal ?? ""));
+      }
+
+      return ascending ? comparison : -comparison;
+    };
+  }, [sortColumn, ascending]);
+
+  return { sortColumn, ascending, toggleSort, sortFn };
+}

From 204cd8515259c42ef7a0e60089448b73a646ee93 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:56:13 -0700
Subject: [PATCH 065/173] Frontend: Add SSE hooks

---
 frontend/src/hooks/useSSE.ts | 52 ++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 frontend/src/hooks/useSSE.ts

diff --git a/frontend/src/hooks/useSSE.ts b/frontend/src/hooks/useSSE.ts
new file mode 100644
index 0000000..3bf7c02
--- /dev/null
+++ b/frontend/src/hooks/useSSE.ts
@@ -0,0 +1,52 @@
+/**
+ * Generic hook for consuming Server-Sent Events (SSE) from a finite stream.
+ *
+ * Creates an EventSource when `url` is non-null; closes on cleanup or when
+ * the stream ends. No auto-reconnect — our SSE streams are finite.
+ */
+
+import { useEffect, useRef } from "react";
+
+export interface UseSSEOptions {
+  /** URL to connect to. Pass `null` to stay disconnected. */
+  url: string | null;
+  /** Called for every `data:` line (already JSON-parsed). */
+  onMessage: (data: unknown) => void;
+  /** Called on EventSource errors. */
+  onError?: (error: Event) => void;
+}
+
+export function useSSE({ url, onMessage, onError }: UseSSEOptions): void {
+  // Store latest callbacks in refs so we never re-open a connection just
+  // because the caller created a new closure.
+  const onMessageRef = useRef(onMessage);
+  const onErrorRef = useRef(onError);
+  onMessageRef.current = onMessage;
+  onErrorRef.current = onError;
+
+  useEffect(() => {
+    if (!url) return;
+
+    const es = new EventSource(url);
+
+    es.onmessage = (event: MessageEvent) => {
+      try {
+        const data: unknown = JSON.parse(event.data as string);
+        onMessageRef.current(data);
+      } catch {
+        // Ignore non-JSON messages (e.g., keep-alive pings)
+      }
+    };
+
+    es.onerror = (event: Event) => {
+      onErrorRef.current?.(event);
+      // The server closes the stream on terminal events, which fires an error
+      // event with readyState CLOSED. We just close our side too.
+      es.close();
+    };
+
+    return () => {
+      es.close();
+    };
+  }, [url]);
+}

From cc2d6fa8a7f3923e74b89e2bd43a6fb389a10f06 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:56:51 -0700
Subject: [PATCH 066/173] Frontend: Add upload job hooks

---
 frontend/src/hooks/useUploadJob.ts | 285 +++++++++++++++++++++++++++++
 1 file changed, 285 insertions(+)
 create mode 100644 frontend/src/hooks/useUploadJob.ts

diff --git a/frontend/src/hooks/useUploadJob.ts b/frontend/src/hooks/useUploadJob.ts
new file mode 100644
index 0000000..4429fb6
--- /dev/null
+++ b/frontend/src/hooks/useUploadJob.ts
@@ -0,0 +1,285 @@
+/**
+ * Hook that wraps bulk-analyze + auto-upload SSE progress.
+ *
+ * The SSE stream has two phases (analysis then upload) but this hook
+ * exposes a single, simple interface. During upload only "active" files
+ * (status=uploading|analyzing) are tracked — the full file list arrives
+ * only in the terminal event and is stored in uploadStore.completedJob.
+ */
+
+import { useCallback, useMemo, useRef, useState } from "react";
+
+import { apiPost } from "../api/client.ts";
+import { useUploadStore } from "../stores/uploadStore.ts";
+import type {
+  AnalysisCompleteEvent,
+  AnalysisProgressEvent,
+  AutoUploadStartingEvent,
+  FileUploadState,
+  UploadJob,
+  UploadJobProgress,
+} from "../types/api.ts";
+import { useSSE } from "./useSSE.ts";
+
+interface StatusCounts {
+  uploaded: number;
+  skipped: number;
+  failed: number;
+}
+
+interface UseUploadJobResult {
+  startUpload: (
+    filePaths: string[],
+    skipDuplicates?: boolean,
+  ) => Promise<void>;
+  cancelUpload: () => Promise<void>;
+  filesProcessed: number;
+  totalFiles: number;
+  activeFiles: FileUploadState[];
+  statusCounts: StatusCounts;
+  progressPercent: number;
+  eta: number | null;
+  isRunning: boolean;
+  uploadedBytesFormatted: string;
+  totalBytesFormatted: string;
+  /** Per-file SSE callback ref — wire to FileStore.updateFile. */
+  onFileUpdate: React.MutableRefObject<((file: FileUploadState) => void) | null>;
+  /** Completion callback ref — wire to FileStore.mergeCompletion. */
+  onCompletion: React.MutableRefObject<((files: FileUploadState[]) => void) | null>;
+}
+
+type SSEEvent =
+  | AnalysisProgressEvent
+  | AnalysisCompleteEvent
+  | AutoUploadStartingEvent
+  | UploadJobProgress
+  | UploadJob;
+
+/** Type guard: does this look like a progress dict (lightweight, during upload)? */
+function isProgressDict(data: Record<string, unknown>): data is UploadJobProgress & Record<string, unknown> {
+  return "job_id" in data && "total_files" in data && !("total_bytes" in data) && !("type" in data);
+}
+
+/** Type guard: does this look like a full UploadJob dict (terminal)? */
+function isFullJobDict(data: Record<string, unknown>): data is UploadJob & Record<string, unknown> {
+  return "job_id" in data && "total_bytes" in data && !("type" in data);
+}
+
+export function useUploadJob(): UseUploadJobResult {
+  const [jobId, setJobId] = useState<string | null>(null);
+  const [isRunning, setIsRunning] = useState(false);
+  const [filesProcessed, setFilesProcessed] = useState(0);
+  const [totalFiles, setTotalFiles] = useState(0);
+  const [activeFiles, setActiveFiles] = useState<FileUploadState[]>([]);
+  const [statusCounts, setStatusCounts] = useState<StatusCounts>({
+    uploaded: 0,
+    skipped: 0,
+    failed: 0,
+  });
+  const [progressPercent, setProgressPercent] = useState(0);
+  const [eta, setEta] = useState<number | null>(null);
+  const [uploadedBytesFormatted, setUploadedBytesFormatted] = useState("");
+  const [totalBytesFormatted, setTotalBytesFormatted] = useState("");
+
+  const { setUploadJobId, setCompletedJob } = useUploadStore();
+
+  // Callback refs for per-file updates — wired by UploadPage to FileStore
+  const onFileUpdateRef = useRef<((file: FileUploadState) => void) | null>(null);
+  const onCompletionRef = useRef<((files: FileUploadState[]) => void) | null>(null);
+
+  /** Handle each SSE event. */
+  const handleMessage = useCallback(
+    (raw: unknown) => {
+      const data = raw as SSEEvent & Record<string, unknown>;
+      if (!data || typeof data !== "object") return;
+
+      // Typed events (analysis phase)
+      if ("type" in data) {
+        switch (data.type) {
+          case "analysis_progress": {
+            const evt = data as AnalysisProgressEvent;
+            setTotalFiles(evt.total_files);
+            // Show the file being analyzed as an active file.
+            setActiveFiles((prev) => {
+              const filtered = prev.filter(
+                (f) => f.local_path !== evt.file.local_path,
+              );
+              if (
+                evt.file.status === "analyzing" ||
+                evt.file.status === "uploading"
+              ) {
+                return [...filtered, evt.file];
+              }
+              return filtered;
+            });
+            // Notify unified table
+            onFileUpdateRef.current?.(evt.file);
+            break;
+          }
+
+          case "analysis_complete": {
+            const evt = data as AnalysisCompleteEvent;
+            setTotalFiles(evt.job.total_files);
+            // If not auto-uploading, this is terminal.
+            if (!evt.auto_upload) {
+              setIsRunning(false);
+              setJobId(null);
+              setCompletedJob(evt.job);
+            }
+            // Clear active files from analysis phase.
+            setActiveFiles([]);
+            break;
+          }
+
+          case "auto_upload_starting":
+            // Upload phase beginning — keep running, active files will
+            // arrive via progress dicts.
+            break;
+
+          default:
+            break;
+        }
+        return;
+      }
+
+      // Lightweight progress dict (during upload)
+      if (isProgressDict(data)) {
+        const p = data as UploadJobProgress;
+        setFilesProcessed(p.files_completed);
+        setTotalFiles(p.total_files);
+        setStatusCounts({
+          uploaded: p.files_uploaded,
+          skipped: p.files_skipped,
+          failed: p.files_failed,
+        });
+        setProgressPercent(p.progress_percent);
+        setEta(p.eta_seconds);
+        setActiveFiles(p.files);
+        setUploadedBytesFormatted(p.uploaded_bytes_formatted);
+        setTotalBytesFormatted(p.total_bytes_formatted);
+
+        // Notify unified table for each active file
+        if (onFileUpdateRef.current) {
+          for (const file of p.files) {
+            onFileUpdateRef.current(file);
+          }
+        }
+
+        // Terminal statuses in progress dict
+        if (
+          p.status === "completed" ||
+          p.status === "failed" ||
+          p.status === "cancelled"
+        ) {
+          setIsRunning(false);
+          setJobId(null);
+        }
+        return;
+      }
+
+      // Full job dict (terminal event)
+      if (isFullJobDict(data)) {
+        const job = data as UploadJob;
+        setFilesProcessed(job.files_completed);
+        setTotalFiles(job.total_files);
+        setStatusCounts({
+          uploaded: job.files_uploaded,
+          skipped: job.files_skipped,
+          failed: job.files_failed,
+        });
+        setProgressPercent(job.progress_percent);
+        setEta(null);
+        setActiveFiles([]);
+        setUploadedBytesFormatted(job.uploaded_bytes_formatted);
+        setTotalBytesFormatted(job.total_bytes_formatted);
+        setCompletedJob(job);
+        // Notify unified table with all completion data
+        onCompletionRef.current?.(job.files);
+        setIsRunning(false);
+        setJobId(null);
+        return;
+      }
+    },
+    [setCompletedJob],
+  );
+
+  const sseUrl = useMemo(
+    () => (jobId && isRunning ? `/api/upload/progress/${jobId}` : null),
+    [jobId, isRunning],
+  );
+
+  useSSE({
+    url: sseUrl,
+    onMessage: handleMessage,
+    onError: () => {
+      // Stream closed — if we're still "running" the server ended it.
+      if (isRunning) {
+        setIsRunning(false);
+        setJobId(null);
+      }
+    },
+  });
+
+  /** Kick off a bulk-analyze + auto-upload job. */
+  const startUpload = useCallback(
+    async (filePaths: string[], skipDuplicates = true) => {
+      // Reset state
+      setFilesProcessed(0);
+      setTotalFiles(0);
+      setActiveFiles([]);
+      setStatusCounts({ uploaded: 0, skipped: 0, failed: 0 });
+      setProgressPercent(0);
+      setEta(null);
+      setUploadedBytesFormatted("");
+      setTotalBytesFormatted("");
+      setIsRunning(true);
+
+      try {
+        const res = await apiPost<{ job_id: string; total_files: number }>(
+          "/api/upload/bulk-analyze",
+          {
+            file_paths: filePaths,
+            auto_upload: true,
+            skip_duplicates: skipDuplicates,
+          },
+        );
+        setUploadJobId(res.job_id);
+        setTotalFiles(res.total_files);
+        setJobId(res.job_id);
+      } catch {
+        setIsRunning(false);
+      }
+    },
+    [setUploadJobId],
+  );
+
+  /** Cancel the current upload job. */
+  const cancelUpload = useCallback(async () => {
+    const currentJobId = useUploadStore.getState().uploadJobId;
+    if (currentJobId) {
+      try {
+        await apiPost(`/api/upload/cancel/${currentJobId}`);
+      } catch {
+        // Ignore
+      }
+    }
+    setIsRunning(false);
+    setJobId(null);
+  }, []);
+
+  return {
+    startUpload,
+    cancelUpload,
+    filesProcessed,
+    totalFiles,
+    activeFiles,
+    statusCounts,
+    progressPercent,
+    eta,
+    isRunning,
+    uploadedBytesFormatted,
+    totalBytesFormatted,
+    onFileUpdate: onFileUpdateRef,
+    onCompletion: onCompletionRef,
+  };
+}

From 0be684269fa18348ee8b1f7f2823dae55eb46bf3 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:57:10 -0700
Subject: [PATCH 067/173] Frontend: Add pagination hook

---
 frontend/src/hooks/usePagination.ts | 66 +++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 frontend/src/hooks/usePagination.ts

diff --git a/frontend/src/hooks/usePagination.ts b/frontend/src/hooks/usePagination.ts
new file mode 100644
index 0000000..5997bd6
--- /dev/null
+++ b/frontend/src/hooks/usePagination.ts
@@ -0,0 +1,66 @@
+import { useCallback, useMemo, useState } from "react";
+
+export interface UsePaginationResult {
+  offset: number;
+  limit: number;
+  currentPage: number;
+  totalPages: number;
+  setTotal: (total: number) => void;
+  goToPage: (page: number) => void;
+  nextPage: () => void;
+  prevPage: () => void;
+  reset: () => void;
+}
+
+export function usePagination(pageSize = 100): UsePaginationResult {
+  const [currentPage, setCurrentPage] = useState(1);
+  const [total, setTotalRaw] = useState(0);
+
+  const totalPages = useMemo(
+    () => Math.max(1, Math.ceil(total / pageSize)),
+    [total, pageSize],
+  );
+
+  const offset = (currentPage - 1) * pageSize;
+
+  const setTotal = useCallback(
+    (newTotal: number) => {
+      setTotalRaw(newTotal);
+      // Clamp current page if total shrinks
+      const newTotalPages = Math.max(1, Math.ceil(newTotal / pageSize));
+      setCurrentPage((prev) => Math.min(prev, newTotalPages));
+    },
+    [pageSize],
+  );
+
+  const goToPage = useCallback(
+    (page: number) => {
+      setCurrentPage(Math.max(1, Math.min(page, totalPages)));
+    },
+    [totalPages],
+  );
+
+  const nextPage = useCallback(() => {
+    setCurrentPage((prev) => Math.min(prev + 1, totalPages));
+  }, [totalPages]);
+
+  const prevPage = useCallback(() => {
+    setCurrentPage((prev) => Math.max(prev - 1, 1));
+  }, []);
+
+  const reset = useCallback(() => {
+    setCurrentPage(1);
+  }, []);
+
+  return {
+    offset,
+    limit: pageSize,
+    currentPage,
+    totalPages,
+    setTotal,
+    goToPage,
+    nextPage,
+    prevPage,
+    reset,
+  };
+}

From bec1ba8828423a818bccbaba1c7766ee8de4c09a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:57:52 -0700
Subject: [PATCH 068/173] Frontend: Add file store hooks

---
 frontend/src/hooks/useFileStore.ts | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 frontend/src/hooks/useFileStore.ts

diff --git a/frontend/src/hooks/useFileStore.ts b/frontend/src/hooks/useFileStore.ts
new file mode 100644
index 0000000..1cdbc18
--- /dev/null
+++ b/frontend/src/hooks/useFileStore.ts
@@ -0,0 +1,19 @@
+/**
+ * Thin hook wrapper around the FileStore singleton.
+ *
+ * Uses useSyncExternalStore so React re-renders only when the
+ * store's snapshot reference changes (rAF-batched).
+ */
+
+import { useSyncExternalStore } from "react";
+
+import { fileStore } from "../stores/fileStore.ts";
+import type { UnifiedFileRow } from "../types/upload.ts";
+
+export function useFileStore(): {
+  files: UnifiedFileRow[];
+  store: typeof fileStore;
+} {
+  const files = useSyncExternalStore(fileStore.subscribe, fileStore.getSnapshot);
+  return { files, store: fileStore };
+}

From c30b616ad21fee1840b89389e4533903b6d8d4e7 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 15:58:20 -0700
Subject: [PATCH 069/173] Frontend: Add delete job hooks

---
 frontend/src/hooks/useDeleteJob.ts | 180 +++++++++++++++++++++++++++++
 1 file changed, 180 insertions(+)
 create mode 100644 frontend/src/hooks/useDeleteJob.ts

diff --git a/frontend/src/hooks/useDeleteJob.ts b/frontend/src/hooks/useDeleteJob.ts
new file mode 100644
index 0000000..e02823d
--- /dev/null
+++ b/frontend/src/hooks/useDeleteJob.ts
@@ -0,0 +1,180 @@
+/**
+ * Hook for managing delete job execution and SSE progress.
+ *
+ * Mirrors the useUploadJob pattern: starts a delete job via POST,
+ * then listens on SSE for per-file progress updates.
+ */
+
+import { useCallback, useMemo, useState } from "react";
+
+import { apiPost } from "../api/client.ts";
+import { useDeleteStore } from "../stores/deleteStore.ts";
+import type {
+  DeleteCompleteEvent,
+  DeleteJobResult,
+  DeleteProgressEvent,
+} from "../types/delete.ts";
+import { useSSE } from "./useSSE.ts";
+
+interface StatusCounts {
+  deleted: number;
+  mismatch: number;
+  failed: number;
+  verified: number;
+  verifying: number;
+}
+
+interface UseDeleteJobResult {
+  startDelete: () => Promise<void>;
+  cancelDelete: () => Promise<void>;
+  filesProcessed: number;
+  totalFiles: number;
+  statusCounts: StatusCounts;
+  totalDeletedSize: number;
+  isRunning: boolean;
+  jobStatus: string;
+}
+
+/** Type guard: is this a progress event? */
+function isProgressEvent(
+  data: Record<string, unknown>,
+): data is DeleteProgressEvent & Record<string, unknown> {
+  return data.type === "delete_progress";
+}
+
+/** Type guard: is this a completion event? */
+function isCompleteEvent(
+  data: Record<string, unknown>,
+): data is DeleteCompleteEvent & Record<string, unknown> {
+  return data.type === "delete_complete";
+}
+
+function extractCounts(counts: Record<string, number>): StatusCounts {
+  return {
+    deleted: counts.deleted ?? 0,
+    mismatch: counts.mismatch ?? 0,
+    failed: counts.failed ?? 0,
+    verified: counts.verified ?? 0,
+    verifying: counts.verifying ?? 0,
+  };
+}
+
+export function useDeleteJob(): UseDeleteJobResult {
+  const [isRunning, setIsRunning] = useState(false);
+  const [filesProcessed, setFilesProcessed] = useState(0);
+  const [totalFiles, setTotalFiles] = useState(0);
+  const [statusCounts, setStatusCounts] = useState<StatusCounts>({
+    deleted: 0,
+    mismatch: 0,
+    failed: 0,
+    verified: 0,
+    verifying: 0,
+  });
+  const [totalDeletedSize, setTotalDeletedSize] = useState(0);
+  const [jobStatus, setJobStatus] = useState("pending");
+  const [activeJobId, setActiveJobId] = useState<string | null>(null);
+
+  const { deleteJobId, setCompletedJob, setIsDeleting } = useDeleteStore();
+
+  const handleMessage = useCallback(
+    (raw: unknown) => {
+      const data = raw as Record<string, unknown>;
+      if (!data || typeof data !== "object") return;
+
+      if (isProgressEvent(data)) {
+        const p = data as DeleteProgressEvent;
+        setFilesProcessed(p.files_processed);
+        setTotalFiles(p.total_files);
+        setStatusCounts(extractCounts(p.status_counts));
+        setTotalDeletedSize(p.total_deleted_size);
+        setJobStatus(p.status);
+        return;
+      }
+
+      if (isCompleteEvent(data)) {
+        const c = data as DeleteCompleteEvent;
+        setFilesProcessed(c.total_files);
+        setTotalFiles(c.total_files);
+        setStatusCounts(extractCounts(c.status_counts));
+        setTotalDeletedSize(c.total_deleted_size);
+        setJobStatus(c.status);
+        setIsRunning(false);
+        setIsDeleting(false);
+        setActiveJobId(null);
+        setCompletedJob(c as unknown as DeleteJobResult);
+        return;
+      }
+    },
+    [setCompletedJob, setIsDeleting],
+  );
+
+  const sseUrl = useMemo(
+    () =>
+      activeJobId && isRunning
+        ? `/api/delete/progress/${activeJobId}`
+        : null,
+    [activeJobId, isRunning],
+  );
+
+  useSSE({
+    url: sseUrl,
+    onMessage: handleMessage,
+    onError: () => {
+      if (isRunning) {
+        setIsRunning(false);
+        setIsDeleting(false);
+        setActiveJobId(null);
+      }
+    },
+  });
+
+  const startDelete = useCallback(async () => {
+    if (!deleteJobId) return;
+
+    setFilesProcessed(0);
+    setStatusCounts({
+      deleted: 0,
+      mismatch: 0,
+      failed: 0,
+      verified: 0,
+      verifying: 0,
+    });
+    setTotalDeletedSize(0);
+    setJobStatus("verifying");
+    setIsRunning(true);
+    setIsDeleting(true);
+
+    try {
+      await apiPost(`/api/delete/start/${deleteJobId}`);
+      setActiveJobId(deleteJobId);
+    } catch {
+      setIsRunning(false);
+      setIsDeleting(false);
+    }
+  }, [deleteJobId, setIsDeleting]);
+
+  const cancelDelete = useCallback(async () => {
+    const jobId = useDeleteStore.getState().deleteJobId;
+    if (jobId) {
+      try {
+        await apiPost(`/api/delete/cancel/${jobId}`);
+      } catch {
+        // Ignore
+      }
+    }
+    setIsRunning(false);
+    setIsDeleting(false);
+    setActiveJobId(null);
+  }, [setIsDeleting]);
+
+  return {
+    startDelete,
+    cancelDelete,
+    filesProcessed,
+    totalFiles,
+    statusCounts,
+    totalDeletedSize,
+    isRunning,
+    jobStatus,
+  };
+}

From 8d576a10a2b53e55c009457e655043ca836de3b4 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:01:02 -0700
Subject: [PATCH 070/173] Frontend: Add delete scan hooks

---
 frontend/src/hooks/useDeleteScan.ts | 40 +++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 frontend/src/hooks/useDeleteScan.ts

diff --git a/frontend/src/hooks/useDeleteScan.ts b/frontend/src/hooks/useDeleteScan.ts
new file mode 100644
index 0000000..cecdcd6
--- /dev/null
+++ b/frontend/src/hooks/useDeleteScan.ts
@@ -0,0 +1,40 @@
+/**
+ * Hook for scanning a folder for deletable MCAP files.
+ *
+ * Calls POST /api/delete/scan and returns scanned files
+ * that match entries in the upload cache.
+ */
+
+import { useCallback } from "react";
+
+import { apiPost } from "../api/client.ts";
+import { useDeleteStore } from "../stores/deleteStore.ts";
+import type { DeleteScanResponse } from "../types/delete.ts";
+
+interface UseDeleteScanResult {
+  scan: (folderPath: string) => Promise<void>;
+  isScanning: boolean;
+}
+
+export function useDeleteScan(): UseDeleteScanResult {
+  const { isScanning, setIsScanning, setScanResults, setDeleteJobId } =
+    useDeleteStore();
+
+  const scan = useCallback(
+    async (folderPath: string) => {
+      setIsScanning(true);
+      try {
+        const res = await apiPost<DeleteScanResponse>("/api/delete/scan", {
+          folder_path: folderPath,
+        });
+        setDeleteJobId(res.job_id);
+        setScanResults(res.files, res.total_size);
+      } finally {
+        setIsScanning(false);
+      }
+    },
+    [setIsScanning, setScanResults, setDeleteJobId],
+  );
+
+  return { scan, isScanning };
+}

From bcf3ab1969ed8151f5044da33c323354579c93c5 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:14:47 -0700
Subject: [PATCH 071/173] Frontend: add plus icon

---
 frontend/src/utils/icons.tsx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
index 1ab5b52..7fcfeec 100644
--- a/frontend/src/utils/icons.tsx
+++ b/frontend/src/utils/icons.tsx
@@ -26,6 +26,7 @@ import {
   RefreshCw,
   XCircle,
   Loader2,
+  Plus,
   type LucideProps,
 } from "lucide-react";
 
@@ -52,6 +53,7 @@ export const SettingsIcon = Settings;
 export const RefreshIcon = RefreshCw;
 export const XCircleIcon = XCircle;
 export const SpinnerIcon = Loader2;
+export const PlusIcon = Plus;
 
 // Export type for icon props
 export type { LucideProps as IconProps };

From 689c1d6b42ade41bc3037430c1a6ce911061d189 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:24:49 -0700
Subject: [PATCH 072/173] Clean: Remove S3 file search

---
 app/routes/files.py       | 52 ---------------------------------------
 frontend/src/types/api.ts |  8 ------
 tests/test_routes.py      | 43 --------------------------------
 3 files changed, 103 deletions(-)

diff --git a/app/routes/files.py b/app/routes/files.py
index fb19351..61b9d78 100644
--- a/app/routes/files.py
+++ b/app/routes/files.py
@@ -102,58 +102,6 @@ def get_file_info() -> tuple[Response, int]:
         return jsonify({"error": str(e)}), 500
 
 
-@files_bp.route("/search", methods=["GET"])
-def search_files() -> tuple[Response, int]:
-    """Search for files in S3 bucket by name pattern.
-
-    Query parameters:
-        query: Search query string
-        prefix: S3 prefix to search within (default: "")
-
-    Returns:
-        JSON response with matching files
-    """
-    query = request.args.get("query", "").lower()
-    prefix = request.args.get("prefix", "")
-
-    if not query:
-        return jsonify({"error": "Search query required"}), 400
-
-    try:
-        client = s3_service.create_s3_client(
-            g.settings.aws_profile,
-            g.settings.aws_region,
-        )
-
-        # List all objects with prefix (no delimiter to get all files)
-        result = s3_service.list_bucket_objects(
-            client,
-            g.settings.s3_bucket,
-            prefix=prefix,
-            delimiter="",  # No delimiter to get all nested files
-            max_keys=10000,
-        )
-
-        if not result["success"]:
-            return jsonify({"error": result["error"]}), 500
-
-        # Filter files by query
-        matching_files = [f for f in result["files"] if query in f["name"].lower()]
-
-        return jsonify(
-            {
-                "success": True,
-                "query": query,
-                "prefix": prefix,
-                "files": matching_files[:100],  # Limit results
-                "total_matches": len(matching_files),
-            }
-        ), 200
-
-    except Exception as e:
-        return jsonify({"error": str(e)}), 500
-
-
 @files_bp.route("/browse", methods=["GET"])
 def browse_local() -> tuple[Response, int]:
     """Browse local filesystem for folder selection.
diff --git a/frontend/src/types/api.ts b/frontend/src/types/api.ts
index fbc3c03..a2e6d2f 100644
--- a/frontend/src/types/api.ts
+++ b/frontend/src/types/api.ts
@@ -246,14 +246,6 @@ export interface S3Breadcrumb {
   prefix: string;
 }
 
-export interface S3SearchResponse {
-  success: boolean;
-  query: string;
-  prefix: string;
-  files: S3File[];
-  total_matches: number;
-}
-
 // ── Settings types ──
 
 export interface AppSettings {
diff --git a/tests/test_routes.py b/tests/test_routes.py
index 9c9b1c8..da87d12 100644
--- a/tests/test_routes.py
+++ b/tests/test_routes.py
@@ -199,49 +199,6 @@ def test_list_files_no_bucket(self, client: FlaskClient) -> None:
         response = client.get("/api/files/list")
         assert response.status_code == 400
 
-    def test_search_no_query(self, client: FlaskClient) -> None:
-        """Test search without query parameter."""
-        # Ensure bucket is set for this test
-        client.put(
-            "/api/settings",
-            data=json.dumps({"s3_bucket": "test-bucket"}),
-            content_type="application/json",
-        )
-
-        response = client.get("/api/files/search")
-        assert response.status_code == 400
-
-    @patch("app.routes.files.s3_service")
-    def test_search_success(self, mock_s3: MagicMock, client: FlaskClient) -> None:
-        """Test successful file search."""
-        # Ensure bucket is set
-        client.put(
-            "/api/settings",
-            data=json.dumps({"s3_bucket": "test-bucket"}),
-            content_type="application/json",
-        )
-
-        mock_s3.create_s3_client.return_value = MagicMock()
-        mock_s3.list_bucket_objects.return_value = {
-            "success": True,
-            "bucket": "test-bucket",
-            "prefix": "",
-            "folders": [],
-            "files": [
-                {"name": "test_file.mcap", "key": "path/test_file.mcap", "size": 1000},
-                {"name": "other.mcap", "key": "path/other.mcap", "size": 2000},
-            ],
-            "error": None,
-        }
-
-        response = client.get("/api/files/search?query=test")
-        assert response.status_code == 200
-
-        data = json.loads(response.data)
-        assert data["success"] is True
-        assert len(data["files"]) == 1
-        assert data["files"][0]["name"] == "test_file.mcap"
-
     def test_get_file_info_no_key(self, client: FlaskClient) -> None:
         """Test getting file info without key parameter."""
         response = client.get("/api/files/info")

From 1353808570d8d591f20b15e13793ec0c4af03f67 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:27:46 -0700
Subject: [PATCH 073/173] Frontend: Add File List component

---
 frontend/src/components/files/FileList.tsx | 70 ++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 frontend/src/components/files/FileList.tsx

diff --git a/frontend/src/components/files/FileList.tsx b/frontend/src/components/files/FileList.tsx
new file mode 100644
index 0000000..619dd06
--- /dev/null
+++ b/frontend/src/components/files/FileList.tsx
@@ -0,0 +1,70 @@
+import type { S3File, S3Folder } from "../../types/api.ts";
+import { FolderIcon, FileIcon } from "../../utils/icons.tsx";
+
+function formatBytes(bytes: number): string {
+  if (bytes === 0) return "0 B";
+  const units = ["B", "KB", "MB", "GB", "TB"];
+  const i = Math.floor(Math.log(bytes) / Math.log(1024));
+  return `${(bytes / 1024 ** i).toFixed(i === 0 ? 0 : 1)} ${units[i]}`;
+}
+
+function formatDate(iso: string): string {
+  const d = new Date(iso);
+  return d.toLocaleDateString(undefined, {
+    year: "numeric",
+    month: "short",
+    day: "numeric",
+    hour: "2-digit",
+    minute: "2-digit",
+  });
+}
+
+interface FileListProps {
+  folders: S3Folder[];
+  files: S3File[];
+  onNavigate: (prefix: string) => void;
+}
+
+export default function FileList({ folders, files, onNavigate }: FileListProps) {
+  if (folders.length === 0 && files.length === 0) {
+    return (
+      <div className="text-center py-12 text-gray-500">
+        <FolderIcon className="mx-auto h-12 w-12 text-gray-300 mb-3" />
+        <p className="text-sm">No files or folders found at this location.</p>
+      </div>
+    );
+  }
+
+  return (
+    <div className="divide-y divide-gray-100">
+      {folders.map((folder) => (
+        <button
+          key={folder.prefix}
+          onClick={() => onNavigate(folder.prefix)}
+          className="w-full flex items-center gap-3 px-4 py-3 hover:bg-gray-50 text-left transition-colors"
+        >
+          <FolderIcon className="h-5 w-5 text-nlr-yellow" />
+          <span className="text-sm font-medium text-gray-900">{folder.name}</span>
+        </button>
+      ))}
+
+      {files.map((file) => (
+        <div
+          key={file.key}
+          className="flex items-center gap-3 px-4 py-3 hover:bg-gray-50 transition-colors"
+        >
+          <FileIcon className="h-5 w-5 text-gray-400" />
+          <div className="flex-1 min-w-0">
+            <p className="text-sm font-medium text-gray-900 truncate" title={file.name}>
+              {file.name}
+            </p>
+          </div>
+          <span className="text-xs text-gray-500 whitespace-nowrap">{formatBytes(file.size)}</span>
+          <span className="text-xs text-gray-400 whitespace-nowrap">
+            {formatDate(file.last_modified)}
+          </span>
+        </div>
+      ))}
+    </div>
+  );
+}

From e2b0acdecd379b6a45ca160ad71b9dc8a5bd12ea Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:28:07 -0700
Subject: [PATCH 074/173] Frontend: Add S3Browser component

---
 frontend/src/components/files/S3Browser.tsx | 120 ++++++++++++++++++++
 1 file changed, 120 insertions(+)
 create mode 100644 frontend/src/components/files/S3Browser.tsx

diff --git a/frontend/src/components/files/S3Browser.tsx b/frontend/src/components/files/S3Browser.tsx
new file mode 100644
index 0000000..d20d46d
--- /dev/null
+++ b/frontend/src/components/files/S3Browser.tsx
@@ -0,0 +1,120 @@
+import { useCallback, useEffect, useState } from "react";
+import { apiGet } from "../../api/client.ts";
+import type { S3File, S3Folder, S3ListResponse } from "../../types/api.ts";
+import Breadcrumb from "../common/Breadcrumb.tsx";
+import Spinner from "../common/Spinner.tsx";
+import FileList from "./FileList.tsx";
+
+interface S3BrowserProps {
+  bucketName: string;
+  region: string;
+}
+
+export default function S3Browser({ bucketName, region }: S3BrowserProps) {
+  const [prefix, setPrefix] = useState("");
+  const [folders, setFolders] = useState<S3Folder[]>([]);
+  const [files, setFiles] = useState<S3File[]>([]);
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+
+  // Build breadcrumb items from the current prefix
+  const breadcrumbItems = (() => {
+    const items = [
+      {
+        label: bucketName,
+        onClick: prefix ? () => setPrefix("") : undefined,
+      },
+    ];
+
+    if (prefix) {
+      const parts = prefix.replace(/\/$/, "").split("/");
+      for (let i = 0; i < parts.length; i++) {
+        const partPrefix = parts.slice(0, i + 1).join("/") + "/";
+        const isLast = i === parts.length - 1;
+        items.push({
+          label: parts[i],
+          onClick: isLast ? undefined : () => setPrefix(partPrefix),
+        });
+      }
+    }
+
+    return items;
+  })();
+
+  const fetchObjects = useCallback(async (currentPrefix: string) => {
+    setLoading(true);
+    setError(null);
+    try {
+      const params: Record<string, string> = { delimiter: "/" };
+      if (currentPrefix) params.prefix = currentPrefix;
+      const data = await apiGet<S3ListResponse>("/api/files/list", params);
+      if (!data.success) {
+        setError(data.error ?? "Failed to list objects");
+        return;
+      }
+      setFolders(data.folders);
+      setFiles(data.files);
+    } catch (err) {
+      setError(err instanceof Error ? err.message : "Failed to fetch files");
+    } finally {
+      setLoading(false);
+    }
+  }, []);
+
+  useEffect(() => {
+    void fetchObjects(prefix);
+  }, [prefix, fetchObjects]);
+
+  const navigateToPrefix = useCallback((newPrefix: string) => {
+    setPrefix(newPrefix);
+  }, []);
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200">
+      {/* Header: Bucket info + breadcrumb */}
+      <div className="p-4 border-b border-gray-200">
+        <div className="flex items-center gap-2 mb-2">
+          <svg
+            className="h-5 w-5 text-nlr-blue"
+            fill="none"
+            viewBox="0 0 24 24"
+            stroke="currentColor"
+          >
+            <path
+              strokeLinecap="round"
+              strokeLinejoin="round"
+              strokeWidth={2}
+              d="M3 15a4 4 0 004 4h9a5 5 0 10-.1-9.999 5.002 5.002 0 10-9.78 2.096A4.001 4.001 0 003 15z"
+            />
+          </svg>
+          <span className="text-sm text-gray-500">
+            {bucketName}
+            <span className="ml-2 text-xs text-gray-400">({region})</span>
+          </span>
+        </div>
+        <Breadcrumb items={breadcrumbItems} />
+      </div>
+
+      {/* Content */}
+      <div className="min-h-[300px]">
+        {loading ? (
+          <div className="flex justify-center py-12">
+            <Spinner message="Loading files..." />
+          </div>
+        ) : error ? (
+          <div className="text-center py-12">
+            <p className="text-sm text-red-600 mb-3">{error}</p>
+            <button
+              onClick={() => fetchObjects(prefix)}
+              className="text-sm text-nlr-blue hover:underline"
+            >
+              Retry
+            </button>
+          </div>
+        ) : (
+          <FileList folders={folders} files={files} onNavigate={navigateToPrefix} />
+        )}
+      </div>
+    </div>
+  );
+}

From cd959578c9e648a9cdf7b2bd408bacc6b8351cf8 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:29:02 -0700
Subject: [PATCH 075/173] Frontend: Add NLR Branded components

---
 frontend/src/components/layout/Footer.tsx | 60 ++++++++++++++++++++++
 frontend/src/components/layout/Header.tsx | 20 ++++++++
 frontend/src/components/layout/Layout.tsx | 24 +++++++++
 frontend/src/components/layout/NavBar.tsx | 61 +++++++++++++++++++++++
 4 files changed, 165 insertions(+)
 create mode 100644 frontend/src/components/layout/Footer.tsx
 create mode 100644 frontend/src/components/layout/Header.tsx
 create mode 100644 frontend/src/components/layout/Layout.tsx
 create mode 100644 frontend/src/components/layout/NavBar.tsx

diff --git a/frontend/src/components/layout/Footer.tsx b/frontend/src/components/layout/Footer.tsx
new file mode 100644
index 0000000..2a643a4
--- /dev/null
+++ b/frontend/src/components/layout/Footer.tsx
@@ -0,0 +1,60 @@
+export default function Footer() {
+  return (
+    <footer className="nlr-footer mt-auto">
+      {/* Footer Top */}
+      <div className="nlr-footer-top">
+        <div className="max-w-5xl mx-auto px-4">
+          <div className="flex flex-col md:flex-row justify-between items-start md:items-center">
+            <div>
+              <a href="https://www.nlr.gov" className="font-bold">
+                National Laboratory of the Rockies
+              </a>
+            </div>
+            <div className="flex flex-wrap gap-4 mt-2 md:mt-0 text-sm">
+              <a href="https://www.nlr.gov/about/">About</a>
+              <a href="https://www.nlr.gov/research/">Research</a>
+              <a href="https://www.nlr.gov/workingwithus/">Work with Us</a>
+              <a href="https://www.nlr.gov/news/">News</a>
+            </div>
+          </div>
+        </div>
+      </div>
+
+      {/* Footer Bottom */}
+      <div className="nlr-footer-bottom">
+        <div className="max-w-5xl mx-auto px-4">
+          <div className="flex flex-col md:flex-row justify-between items-center">
+            <div className="flex items-center gap-6 mb-4 md:mb-0">
+              <a
+                href="https://www.allianceforsustainableenergy.org/"
+                target="_blank"
+                rel="noopener noreferrer"
+              >
+                <img
+                  src="/images/alliance-logo_black.svg"
+                  alt="Alliance for Energy Innovation"
+                  className="h-8"
+                />
+              </a>
+              <a
+                href="https://www.energy.gov"
+                target="_blank"
+                rel="noopener noreferrer"
+              >
+                <img
+                  src="/images/doe-logo.svg"
+                  alt="U.S. Department of Energy"
+                  className="h-10"
+                />
+              </a>
+            </div>
+            <p className="nlr-attr text-center md:text-right max-w-md flex-grow">
+              The National Laboratory of the Rockies is a national laboratory of the
+              U.S. Department of Energy, Office of Critical Minerals and Energy Innovation.
+            </p>
+          </div>
+        </div>
+      </div>
+    </footer>
+  );
+}
diff --git a/frontend/src/components/layout/Header.tsx b/frontend/src/components/layout/Header.tsx
new file mode 100644
index 0000000..171a9c8
--- /dev/null
+++ b/frontend/src/components/layout/Header.tsx
@@ -0,0 +1,20 @@
+import { useAppStore } from "../../stores/appStore.ts";
+
+export default function Header() {
+  const displayName = useAppStore((s) => s.settings?.display_name ?? "MODAQ Upload");
+
+  return (
+    <header className="nlr-header">
+      <div className="nlr-header-top">
+        <h1 className="nlr-header-title">{displayName}</h1>
+        <a href="https://www.nlr.gov" target="_blank" rel="noopener noreferrer">
+          <img
+            src="/images/nlr-logo@2x-01.png"
+            alt="National Laboratory of the Rockies"
+            className="nlr-logo-image"
+          />
+        </a>
+      </div>
+    </header>
+  );
+}
diff --git a/frontend/src/components/layout/Layout.tsx b/frontend/src/components/layout/Layout.tsx
new file mode 100644
index 0000000..24c5add
--- /dev/null
+++ b/frontend/src/components/layout/Layout.tsx
@@ -0,0 +1,24 @@
+import { useState } from "react";
+import { Outlet } from "react-router-dom";
+import NotificationStack from "../common/Notification.tsx";
+import AboutModal from "./AboutModal.tsx";
+import Footer from "./Footer.tsx";
+import Header from "./Header.tsx";
+import NavBar from "./NavBar.tsx";
+
+export default function Layout() {
+  const [aboutOpen, setAboutOpen] = useState(false);
+
+  return (
+    <div className="bg-gray-50 min-h-screen flex flex-col font-[family-name:var(--font-family-roboto)]">
+      <Header />
+      <NavBar onAboutClick={() => setAboutOpen(true)} />
+      <main className="max-w-5xl w-full mx-auto px-4 py-8 flex-grow">
+        <Outlet />
+      </main>
+      <Footer />
+      <AboutModal isOpen={aboutOpen} onClose={() => setAboutOpen(false)} />
+      <NotificationStack />
+    </div>
+  );
+}
diff --git a/frontend/src/components/layout/NavBar.tsx b/frontend/src/components/layout/NavBar.tsx
new file mode 100644
index 0000000..37e7bba
--- /dev/null
+++ b/frontend/src/components/layout/NavBar.tsx
@@ -0,0 +1,61 @@
+import { NavLink } from "react-router-dom";
+import { useAppStore } from "../../stores/appStore.ts";
+
+const navItems = [
+  { to: "/", label: "Upload" },
+  { to: "/files", label: "Browse Uploaded Files" },
+  { to: "/logs", label: "History" },
+];
+
+interface NavBarProps {
+  onAboutClick: () => void;
+}
+
+export default function NavBar({ onAboutClick }: NavBarProps) {
+  const version = useAppStore((s) => s.version?.version);
+
+  return (
+    <nav className="nlr-menu-bar">
+      <div className="nlr-menu-container">
+        {navItems.map((item) => (
+          <NavLink
+            key={item.to}
+            to={item.to}
+            end={item.to === "/"}
+            className={({ isActive }) =>
+              `nlr-menu-item${isActive ? " active" : ""}`
+            }
+          >
+            {item.label}
+          </NavLink>
+        ))}
+        <div className="flex-grow" />
+        {version && (
+          <button
+            onClick={onAboutClick}
+            className="text-xs font-mono bg-nlr-blue text-white px-2 py-1 rounded hover:bg-nlr-blue-light mr-2"
+            title="About this application"
+          >
+            v{version}
+          </button>
+        )}
+        <NavLink
+          to="/delete"
+          className={({ isActive }) =>
+            `nlr-menu-item${isActive ? " active" : ""}`
+          }
+        >
+          Clear Hard Drive
+        </NavLink>
+        <NavLink
+          to="/settings"
+          className={({ isActive }) =>
+            `nlr-menu-item${isActive ? " active" : ""}`
+          }
+        >
+          Settings
+        </NavLink>
+      </div>
+    </nav>
+  );
+}

From 02edd19bff2a99825ca6138cbde87636dc3549df Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:29:26 -0700
Subject: [PATCH 076/173] Frontend: Add application about modal

---
 frontend/src/components/layout/AboutModal.tsx | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 frontend/src/components/layout/AboutModal.tsx

diff --git a/frontend/src/components/layout/AboutModal.tsx b/frontend/src/components/layout/AboutModal.tsx
new file mode 100644
index 0000000..bd29056
--- /dev/null
+++ b/frontend/src/components/layout/AboutModal.tsx
@@ -0,0 +1,48 @@
+import Modal from "../common/Modal.tsx";
+import { useAppStore } from "../../stores/appStore.ts";
+
+interface AboutModalProps {
+  isOpen: boolean;
+  onClose: () => void;
+}
+
+export default function AboutModal({ isOpen, onClose }: AboutModalProps) {
+  const version = useAppStore((s) => s.version);
+
+  return (
+    <Modal
+      isOpen={isOpen}
+      onClose={onClose}
+      title="About"
+      footer={
+        <button
+          onClick={onClose}
+          className="px-4 py-2 bg-nlr-gray text-white rounded hover:opacity-90 text-sm"
+        >
+          Close
+        </button>
+      }
+    >
+      <div className="p-3 bg-gray-50 rounded">
+        <div className="flex justify-between items-center">
+          <span className="text-sm text-gray-500">Version</span>
+          <span className="font-mono text-sm font-semibold">
+            {version?.version ?? "loading..."}
+          </span>
+        </div>
+        <div className="flex justify-between items-center mt-2">
+          <span className="text-sm text-gray-500">Commit</span>
+          <span className="font-mono text-sm text-gray-600">
+            {version?.commit ? version.commit.slice(0, 7) : "-"}
+          </span>
+        </div>
+        <div className="flex justify-between items-center mt-2">
+          <span className="text-sm text-gray-500">Branch</span>
+          <span className="font-mono text-sm text-gray-600">
+            {version?.branch ?? "-"}
+          </span>
+        </div>
+      </div>
+    </Modal>
+  );
+}

From 214048bbcadfce6d2985b95edb016551bd9a0581 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:32:31 -0700
Subject: [PATCH 077/173] Frontend: Add Folder Browser Component

---
 .../src/components/upload/FolderBrowser.tsx   | 726 ++++++++++++++++++
 1 file changed, 726 insertions(+)
 create mode 100644 frontend/src/components/upload/FolderBrowser.tsx

diff --git a/frontend/src/components/upload/FolderBrowser.tsx b/frontend/src/components/upload/FolderBrowser.tsx
new file mode 100644
index 0000000..79b770d
--- /dev/null
+++ b/frontend/src/components/upload/FolderBrowser.tsx
@@ -0,0 +1,726 @@
+/**
+ * Step 1: Filesystem browser for selecting a folder of MCAP files.
+ *
+ * Fetches `GET /api/files/browse?path=...` and renders:
+ * - Quick links sidebar
+ * - Breadcrumb navigation
+ * - Summary bar with file counts + upload button (top, always visible)
+ * - Folder list with upload progress indicators
+ * - MCAP file list with clear uploaded/new status
+ */
+
+import { useCallback, useEffect, useMemo, useState } from "react";
+
+import { apiGet } from "../../api/client.ts";
+import type { BrowseResponse, LocalFile, LocalFolder } from "../../types/api.ts";
+import { formatBytes } from "../../utils/format/bytes.ts";
+import { formatDate } from "../../utils/format/date.ts";
+import Breadcrumb from "../common/Breadcrumb.tsx";
+import Spinner from "../common/Spinner.tsx";
+import {
+  FolderIcon,
+  FileIcon,
+  ChevronRightIcon,
+  CheckIcon,
+  PlusIcon,
+  UploadIcon,
+} from "../../utils/icons.tsx";
+
+type FileSortKey = "filename" | "size" | "mtime" | "status";
+type FileSortDir = "asc" | "desc";
+
+export type BrowserMode = "upload" | "delete";
+
+export interface FolderExclusions {
+  subfolders: string[];
+  files: string[];
+}
+
+interface FolderBrowserProps {
+  onFolderSelected: (folderPath: string, exclusions?: FolderExclusions) => void;
+  initialPath?: string;
+  /** Controls wording, colors, and which files are emphasised. Default: "upload". */
+  mode?: BrowserMode;
+}
+
+/** Mode-dependent text and styling. */
+const modeConfig = {
+  upload: {
+    title: "Select Folder to Upload",
+    subtitle: "Browse to a folder containing MCAP files.",
+    details: "",
+    /** Stat chip shown for the "actionable" count (new files for upload). */
+    actionableLabel: "not uploaded",
+    actionableColor: "green" as const,
+    actionableIcon: "plus" as const,
+    /** Stat chip shown for the "other" count (already uploaded). */
+    otherLabel: "already uploaded",
+    otherColor: "gray" as const,
+    otherIcon: "check" as const,
+    /** Action button wording — count is the "actionable" file count. */
+    buttonLabel: (count: number) =>
+      count > 0 ? `Upload ${count.toLocaleString()} file${count !== 1 ? "s" : ""}` : "Upload This Folder",
+    buttonColor: "bg-nlr-blue text-white hover:bg-blue-700",
+    /** For folders: dim when ALL files are already uploaded (nothing to upload). */
+    dimFolder: (allUploaded: boolean, _noneUploaded: boolean) => allUploaded,
+    /** For file rows: dim files that are already uploaded. */
+    dimFile: (uploaded: boolean) => uploaded,
+    /** Status badge for "uploaded" files. */
+    uploadedBadge: { bg: "bg-green-50 text-green-700 border-green-200", label: "Uploaded" },
+    /** Status badge for "not uploaded" files. */
+    notUploadedBadge: { bg: "bg-amber-50 text-amber-700 border-amber-200", label: "Not Uploaded" },
+  },
+  delete: {
+    title: "Select Folder to Clear",
+    subtitle: "Free up disk space by removing local files that have already been safely uploaded. Each file is verified in the cloud before being removed.",
+    details: "Before removing a local file, the app checks that the uploaded file exists on the cloud server, that its size matches, and compares checksums. A checksum is a unique fingerprint computed from the file's contents — if both fingerprints match, the files are identical.",
+    actionableLabel: "uploaded (deletable)",
+    actionableColor: "green" as const,
+    actionableIcon: "check" as const,
+    otherLabel: "not uploaded",
+    otherColor: "gray" as const,
+    otherIcon: "plus" as const,
+    buttonLabel: (count: number) =>
+      count > 0 ? `Clear ${count.toLocaleString()} file${count !== 1 ? "s" : ""}` : "Select Folder",
+    buttonColor: "bg-red-600 text-white hover:bg-red-700",
+    dimFolder: (_allUploaded: boolean, noneUploaded: boolean) => noneUploaded,
+    dimFile: (uploaded: boolean) => !uploaded,
+    uploadedBadge: { bg: "bg-green-50 text-green-700 border-green-200", label: "Uploaded" },
+    notUploadedBadge: { bg: "bg-gray-100 text-gray-500 border-gray-200", label: "Not Uploaded" },
+  },
+} as const;
+
+export default function FolderBrowser({
+  onFolderSelected,
+  initialPath,
+  mode = "upload",
+}: FolderBrowserProps) {
+  const cfg = modeConfig[mode];
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [data, setData] = useState<BrowseResponse | null>(null);
+  const [checkedFolders, setCheckedFolders] = useState<Set<string>>(new Set());
+  const [checkedFiles, setCheckedFiles] = useState<Set<string>>(new Set());
+  const [searchQuery, setSearchQuery] = useState("");
+  const [selectFirstN, setSelectFirstN] = useState("");
+  const [fileSortKey, setFileSortKey] = useState<FileSortKey>("filename");
+  const [fileSortDir, setFileSortDir] = useState<FileSortDir>("asc");
+
+  const navigate = useCallback(async (path?: string) => {
+    setLoading(true);
+    setError(null);
+    try {
+      const params: Record<string, string> = path ? { path } : {};
+      const res = await apiGet<BrowseResponse>("/api/files/browse", params);
+      setData(res);
+    } catch (err) {
+      setError(err instanceof Error ? err.message : "Failed to browse folder");
+    } finally {
+      setLoading(false);
+    }
+  }, []);
+
+  useEffect(() => {
+    navigate(initialPath);
+  }, [navigate, initialPath]);
+
+  // Reset checked state and search when data changes (new directory loaded)
+  useEffect(() => {
+    if (!data) return;
+    setCheckedFolders(new Set(data.folders.map((f) => f.name)));
+    setCheckedFiles(new Set(data.files.map((f) => f.name)));
+    setSearchQuery("");
+    setSelectFirstN("");
+  }, [data]);
+
+  const breadcrumbItems = (data?.breadcrumbs ?? []).map((b, i, arr) => ({
+    label: b.name,
+    onClick: i < arr.length - 1 ? () => navigate(b.path) : undefined,
+  }));
+
+  const totalMcap = data?.total_mcap_count ?? 0;
+  const alreadyUploaded = data?.already_uploaded ?? 0;
+  const newFiles = totalMcap - alreadyUploaded;
+  const hasFiles = totalMcap > 0;
+
+  // Mode-dependent counts: "actionable" = files the user will act on
+  const actionableCount = mode === "upload" ? newFiles : alreadyUploaded;
+  const otherCount = mode === "upload" ? alreadyUploaded : newFiles;
+
+  const totalItems = (data?.folders.length ?? 0) + (data?.files.length ?? 0);
+  const checkedCount = checkedFolders.size + checkedFiles.size;
+  const allChecked = totalItems > 0 && checkedCount === totalItems;
+
+  const selectAll = useCallback(() => {
+    if (!data) return;
+    setCheckedFolders(new Set(data.folders.map((f) => f.name)));
+    setCheckedFiles(new Set(data.files.map((f) => f.name)));
+  }, [data]);
+
+  const deselectAll = useCallback(() => {
+    setCheckedFolders(new Set());
+    setCheckedFiles(new Set());
+  }, []);
+
+  const toggleFolder = useCallback((name: string) => {
+    setCheckedFolders((prev) => {
+      const next = new Set(prev);
+      if (next.has(name)) next.delete(name);
+      else next.add(name);
+      return next;
+    });
+  }, []);
+
+  const toggleFile = useCallback((name: string) => {
+    setCheckedFiles((prev) => {
+      const next = new Set(prev);
+      if (next.has(name)) next.delete(name);
+      else next.add(name);
+      return next;
+    });
+  }, []);
+
+  // Filtered folders/files based on search query
+  const filteredFolders = useMemo(() => {
+    if (!data || !searchQuery) return data?.folders ?? [];
+    const q = searchQuery.toLowerCase();
+    return data.folders.filter((f) => f.name.toLowerCase().includes(q));
+  }, [data, searchQuery]);
+
+  const filteredFiles = useMemo(() => {
+    if (!data || !searchQuery) return data?.files ?? [];
+    const q = searchQuery.toLowerCase();
+    return data.files.filter((f) => f.name.toLowerCase().includes(q));
+  }, [data, searchQuery]);
+
+  // Sort the filtered files
+  const sortedFiles = useMemo(() => {
+    const sorted = [...filteredFiles];
+    const dir = fileSortDir === "asc" ? 1 : -1;
+    sorted.sort((a, b) => {
+      switch (fileSortKey) {
+        case "filename":
+          return dir * a.name.localeCompare(b.name);
+        case "size":
+          return dir * (a.size - b.size);
+        case "mtime":
+          return dir * (a.mtime - b.mtime);
+        case "status": {
+          const sa = a.already_uploaded ? 1 : 0;
+          const sb = b.already_uploaded ? 1 : 0;
+          return dir * (sa - sb);
+        }
+        default:
+          return 0;
+      }
+    });
+    return sorted;
+  }, [filteredFiles, fileSortKey, fileSortDir]);
+
+  const handleFileSort = useCallback((key: FileSortKey) => {
+    if (fileSortKey === key) {
+      setFileSortDir((d) => (d === "asc" ? "desc" : "asc"));
+    } else {
+      setFileSortKey(key);
+      setFileSortDir("asc");
+    }
+  }, [fileSortKey]);
+
+  const isFiltering = searchQuery.length > 0;
+
+  const selectShown = useCallback(() => {
+    setCheckedFolders(new Set(filteredFolders.map((f) => f.name)));
+    setCheckedFiles(new Set(filteredFiles.map((f) => f.name)));
+  }, [filteredFolders, filteredFiles]);
+
+  const applySelectFirstN = useCallback(() => {
+    const n = Number.parseInt(selectFirstN, 10);
+    if (Number.isNaN(n) || n <= 0) return;
+    setCheckedFolders(new Set());
+    setCheckedFiles(new Set(filteredFiles.slice(0, n).map((f) => f.name)));
+    setSelectFirstN("");
+  }, [selectFirstN, filteredFiles]);
+
+  // Build exclusions from unchecked items
+  const exclusions = useMemo((): FolderExclusions | undefined => {
+    if (!data) return undefined;
+    const uncheckedFolders = data.folders
+      .filter((f) => !checkedFolders.has(f.name))
+      .map((f) => f.name);
+    const uncheckedFiles = data.files
+      .filter((f) => !checkedFiles.has(f.name))
+      .map((f) => f.name);
+    if (uncheckedFolders.length === 0 && uncheckedFiles.length === 0) return undefined;
+    return { subfolders: uncheckedFolders, files: uncheckedFiles };
+  }, [data, checkedFolders, checkedFiles]);
+
+  const handleUploadClick = useCallback(() => {
+    if (!data) return;
+    onFolderSelected(data.current_path, exclusions);
+  }, [data, exclusions, onFolderSelected]);
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200">
+      {/* Header */}
+      <div className="border-b border-gray-200 px-5 py-3">
+        <h3 className="text-lg font-semibold text-gray-900">
+          {cfg.title}
+        </h3>
+        <p className="text-sm text-gray-500 mt-0.5">
+          {cfg.subtitle}
+        </p>
+        {cfg.details && (
+          <details className="mt-1.5">
+            <summary className="text-xs text-nlr-blue cursor-pointer hover:underline select-none">
+              How does verification work?
+            </summary>
+            <p className="text-xs text-gray-500 mt-1 leading-relaxed">
+              {cfg.details}
+            </p>
+          </details>
+        )}
+      </div>
+
+      <div className="flex min-h-[400px]">
+        {/* Quick links sidebar */}
+        <div className="w-48 border-r border-gray-200 bg-gray-50 p-3 flex-shrink-0">
+          <h4 className="text-xs font-semibold text-gray-400 uppercase tracking-wider mb-2">
+            Quick Links
+          </h4>
+          <ul className="space-y-1">
+            {(data?.quick_links ?? []).map((link) => (
+              <li key={link.path}>
+                <button
+                  type="button"
+                  onClick={() => navigate(link.path)}
+                  className="w-full text-left text-sm text-gray-700 hover:text-nlr-blue hover:bg-gray-100 rounded px-2 py-1.5 truncate"
+                  title={link.path}
+                >
+                  <FolderIcon className="inline-block w-4 h-4 mr-1.5 text-gray-400" />
+                  {link.name}
+                </button>
+              </li>
+            ))}
+          </ul>
+        </div>
+
+        {/* Main content area */}
+        <div className="flex-1 flex flex-col min-w-0">
+          {/* Breadcrumbs */}
+          <div className="px-4 py-2 border-b border-gray-100 bg-gray-50/50">
+            <Breadcrumb items={breadcrumbItems} />
+          </div>
+
+          {/* Summary bar — always visible when we have data and MCAP files exist */}
+          {!loading && data && hasFiles && (
+            <div className="px-4 py-3 border-b border-gray-200 bg-white">
+              <div className="flex items-center justify-between gap-4">
+                {/* Stat chips */}
+                <div className="flex items-center gap-3 flex-wrap">
+                  <StatChip
+                    icon={<FileIcon className="w-3.5 h-3.5" />}
+                    value={totalMcap}
+                    label={totalMcap === 1 ? "MCAP file" : "MCAP files"}
+                    color="blue"
+                  />
+                  {actionableCount > 0 && (
+                    <StatChip
+                      icon={cfg.actionableIcon === "plus"
+                        ? <PlusIcon className="w-3.5 h-3.5" />
+                        : <CheckIcon className="w-3.5 h-3.5" />}
+                      value={actionableCount}
+                      label={cfg.actionableLabel}
+                      color={cfg.actionableColor}
+                    />
+                  )}
+                  {otherCount > 0 && (
+                    <StatChip
+                      icon={cfg.otherIcon === "check"
+                        ? <CheckIcon className="w-3.5 h-3.5" />
+                        : <PlusIcon className="w-3.5 h-3.5" />}
+                      value={otherCount}
+                      label={cfg.otherLabel}
+                      color={cfg.otherColor}
+                    />
+                  )}
+                  {totalMcap !== data.mcap_count && (
+                    <span className="text-xs text-gray-400">
+                      includes subfolders
+                    </span>
+                  )}
+                </div>
+
+                {/* Action button */}
+                <button
+                  type="button"
+                  onClick={handleUploadClick}
+                  disabled={checkedCount === 0}
+                  className={`px-5 py-2 rounded text-sm font-medium transition-colors flex-shrink-0
+                    ${cfg.buttonColor}
+                    disabled:bg-gray-300 disabled:text-gray-500 disabled:cursor-not-allowed`}
+                >
+                  {cfg.buttonLabel(actionableCount)}
+                  <ChevronRightIcon className="w-4 h-4 ml-1 inline-block" />
+                </button>
+              </div>
+            </div>
+          )}
+
+          {/* Loading / Error */}
+          {loading && (
+            <div className="flex-1 flex items-center justify-center">
+              <Spinner message="Loading..." />
+            </div>
+          )}
+
+          {error && (
+            <div className="p-4 text-sm text-red-600 bg-red-50 m-4 rounded">
+              {error}
+            </div>
+          )}
+
+          {/* Folder and file list */}
+          {!loading && !error && data && (
+            <div className="flex-1 overflow-auto">
+              {/* Selection toolbar */}
+              {totalItems > 0 && (
+                <div className="space-y-1 px-4 py-1.5 border-b border-gray-100 bg-gray-50/50 text-xs">
+                  <div className="flex items-center gap-3">
+                    <input
+                      type="text"
+                      value={searchQuery}
+                      onChange={(e) => setSearchQuery(e.target.value)}
+                      placeholder="Search files and folders..."
+                      className="border border-gray-300 rounded px-2 py-1 text-xs bg-white w-52"
+                    />
+                    <div className="flex items-center gap-1.5 ml-auto">
+                      <span className="text-gray-400">Select:</span>
+                      <button
+                        type="button"
+                        onClick={selectAll}
+                        disabled={allChecked}
+                        className="text-nlr-blue hover:underline disabled:text-gray-400 disabled:no-underline"
+                      >
+                        All
+                      </button>
+                      {isFiltering && (
+                        <>
+                          <span className="text-gray-300">|</span>
+                          <button
+                            type="button"
+                            onClick={selectShown}
+                            className="text-nlr-blue hover:underline"
+                          >
+                            Shown
+                          </button>
+                        </>
+                      )}
+                      <span className="text-gray-300">|</span>
+                      <button
+                        type="button"
+                        onClick={deselectAll}
+                        disabled={checkedCount === 0}
+                        className="text-nlr-blue hover:underline disabled:text-gray-400 disabled:no-underline"
+                      >
+                        None
+                      </button>
+                    </div>
+                  </div>
+                  {data.files.length > 0 && (
+                    <div className="flex items-center gap-1.5">
+                      <span className="text-gray-400">Select first</span>
+                      <input
+                        type="number"
+                        min="1"
+                        value={selectFirstN}
+                        onChange={(e) => setSelectFirstN(e.target.value)}
+                        onKeyDown={(e) => { if (e.key === "Enter") applySelectFirstN(); }}
+                        placeholder="#"
+                        className="border border-gray-300 rounded px-1.5 py-0.5 text-xs bg-white w-16 tabular-nums"
+                      />
+                      <button
+                        type="button"
+                        onClick={applySelectFirstN}
+                        disabled={!selectFirstN || Number.parseInt(selectFirstN, 10) <= 0}
+                        className="text-nlr-blue hover:underline disabled:text-gray-300 disabled:no-underline"
+                      >
+                        files
+                      </button>
+                      <span className="ml-auto text-gray-400">
+                        {checkedCount} of {totalItems} selected
+                        {isFiltering && ` (${filteredFolders.length + filteredFiles.length} shown)`}
+                      </span>
+                    </div>
+                  )}
+                </div>
+              )}
+
+              {/* Folders */}
+              {filteredFolders.length > 0 && (
+                <FolderList
+                  folders={filteredFolders}
+                  onNavigate={navigate}
+                  checkedFolders={checkedFolders}
+                  onToggleFolder={toggleFolder}
+                  mode={mode}
+                />
+              )}
+
+              {/* Files */}
+              {sortedFiles.length > 0 && (
+                <FileList
+                  files={sortedFiles}
+                  checkedFiles={checkedFiles}
+                  onToggleFile={toggleFile}
+                  sortKey={fileSortKey}
+                  sortDir={fileSortDir}
+                  onSort={handleFileSort}
+                  mode={mode}
+                />
+              )}
+
+              {/* Empty state */}
+              {filteredFolders.length === 0 && filteredFiles.length === 0 && (
+                <div className="flex-1 flex items-center justify-center p-8 text-gray-400 text-sm">
+                  {isFiltering
+                    ? "No items match your search."
+                    : "No folders or MCAP files found here."}
+                </div>
+              )}
+            </div>
+          )}
+
+          {/* Minimal footer showing path */}
+          {!loading && data && (
+            <div className="border-t border-gray-200 px-4 py-2 bg-gray-50">
+              <span className="text-xs text-gray-400 truncate block" title={data.current_path}>
+                {data.current_path}
+              </span>
+            </div>
+          )}
+        </div>
+      </div>
+    </div>
+  );
+}
+
+/* ─── Sub-components ─── */
+
+/** Compact stat chip for the summary bar. */
+function StatChip({
+  icon,
+  value,
+  label,
+  color,
+}: {
+  icon: React.ReactNode;
+  value: number;
+  label: string;
+  color: "blue" | "green" | "gray";
+}) {
+  const colors = {
+    blue: "bg-blue-50 text-blue-700 border-blue-200",
+    green: "bg-green-50 text-green-700 border-green-200",
+    gray: "bg-gray-100 text-gray-600 border-gray-200",
+  };
+  return (
+    <span className={`inline-flex items-center gap-1.5 px-2.5 py-1 rounded-full text-xs font-medium border ${colors[color]}`}>
+      {icon}
+      <span className="tabular-nums font-semibold">{value.toLocaleString()}</span>
+      {label}
+    </span>
+  );
+}
+
+
+function FolderList({
+  folders,
+  onNavigate,
+  checkedFolders,
+  onToggleFolder,
+  mode = "upload",
+}: {
+  folders: LocalFolder[];
+  onNavigate: (path: string) => void;
+  checkedFolders: Set<string>;
+  onToggleFolder: (name: string) => void;
+  mode?: BrowserMode;
+}) {
+  const cfg = modeConfig[mode];
+  return (
+    <div className="divide-y divide-gray-100">
+      {folders.map((folder) => {
+        const allUploaded = folder.mcap_count > 0 && folder.already_uploaded === folder.mcap_count;
+        const someUploaded = folder.already_uploaded > 0 && !allUploaded;
+        const noneUploaded = folder.mcap_count > 0 && folder.already_uploaded === 0;
+        const isDimmed = cfg.dimFolder(allUploaded, noneUploaded);
+
+        return (
+          <div
+            key={folder.path}
+            className={`flex items-center px-4 py-2.5 hover:bg-gray-50 group ${isDimmed ? "opacity-60" : ""}`}
+          >
+            <input
+              type="checkbox"
+              checked={checkedFolders.has(folder.name)}
+              onChange={() => onToggleFolder(folder.name)}
+              className="h-3.5 w-3.5 rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue cursor-pointer flex-shrink-0 mr-2"
+            />
+            <button
+              type="button"
+              onClick={() => onNavigate(folder.path)}
+              className="flex items-center flex-1 min-w-0 text-left"
+            >
+              <FolderIcon className="w-5 h-5 text-amber-400 flex-shrink-0 mr-3" />
+              <span className="text-sm text-gray-800 group-hover:text-nlr-blue truncate flex-1">
+                {folder.name}
+              </span>
+            </button>
+            {folder.mcap_count > 0 && (
+              <span className="ml-2 flex items-center gap-2 flex-shrink-0">
+                {/* Upload status indicator */}
+                {allUploaded && (
+                  <span className="inline-flex items-center gap-1 text-xs text-gray-500">
+                    <CheckIcon className="w-3.5 h-3.5 text-green-500" />
+                    {folder.mcap_count}/{folder.mcap_count} uploaded
+                  </span>
+                )}
+                {someUploaded && (
+                  <span className="inline-flex items-center gap-1.5 text-xs">
+                    <UploadProgress uploaded={folder.already_uploaded} total={folder.mcap_count} />
+                    <span className="text-gray-600">
+                      {folder.already_uploaded}/{folder.mcap_count} uploaded
+                    </span>
+                  </span>
+                )}
+                {noneUploaded && (
+                  <span className="text-xs text-blue-600 font-medium">
+                    {folder.mcap_count} file{folder.mcap_count !== 1 ? "s" : ""}
+                  </span>
+                )}
+              </span>
+            )}
+          </div>
+        );
+      })}
+    </div>
+  );
+}
+
+/** Simple progress bar showing upload fraction. */
+function UploadProgress({ uploaded, total }: { uploaded: number; total: number }) {
+  const pct = total > 0 ? (uploaded / total) * 100 : 0;
+
+  return (
+    <div className="w-12 h-1.5 bg-gray-200 rounded-full overflow-hidden">
+      <div
+        className="h-full bg-amber-500 rounded-full transition-all"
+        style={{ width: `${pct}%` }}
+      />
+    </div>
+  );
+}
+
+function FileList({
+  files,
+  checkedFiles,
+  onToggleFile,
+  sortKey,
+  sortDir,
+  onSort,
+  mode = "upload",
+}: {
+  files: LocalFile[];
+  checkedFiles: Set<string>;
+  onToggleFile: (name: string) => void;
+  sortKey: FileSortKey;
+  sortDir: FileSortDir;
+  onSort: (key: FileSortKey) => void;
+  mode?: BrowserMode;
+}) {
+  const cfg = modeConfig[mode];
+  return (
+    <div>
+      {/* Column headers */}
+      <div className="grid grid-cols-[28px_1fr_80px_100px_120px] gap-2 px-4 py-2 bg-gray-50 border-y border-gray-200 text-xs font-medium text-gray-500 uppercase tracking-wider">
+        <div />
+        <FileSortHeader label="Filename" sortKey="filename" currentKey={sortKey} dir={sortDir} onSort={onSort} />
+        <FileSortHeader label="Size" sortKey="size" currentKey={sortKey} dir={sortDir} onSort={onSort} className="justify-end" />
+        <FileSortHeader label="Modified" sortKey="mtime" currentKey={sortKey} dir={sortDir} onSort={onSort} />
+        <FileSortHeader label="Status" sortKey="status" currentKey={sortKey} dir={sortDir} onSort={onSort} className="justify-center" />
+      </div>
+      {/* File rows */}
+      <div className="divide-y divide-gray-100">
+        {files.map((file) => {
+          const uploaded = file.already_uploaded === true;
+          const isDimmed = cfg.dimFile(uploaded);
+          const badge = uploaded ? cfg.uploadedBadge : cfg.notUploadedBadge;
+          return (
+            <div
+              key={file.path}
+              className={`grid grid-cols-[28px_1fr_80px_100px_120px] gap-2 px-4 py-2 items-center text-sm hover:bg-gray-50/50 ${isDimmed ? "bg-gray-50/30" : ""}`}
+            >
+              <input
+                type="checkbox"
+                checked={checkedFiles.has(file.name)}
+                onChange={() => onToggleFile(file.name)}
+                className="h-3.5 w-3.5 rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue cursor-pointer"
+              />
+              <span className={`truncate ${isDimmed ? "text-gray-400" : "text-gray-800"}`}>
+                {file.name}
+              </span>
+              <span className="text-gray-400 text-xs text-right tabular-nums">
+                {formatBytes(file.size)}
+              </span>
+              <span className="text-gray-400 text-xs">
+                {formatDate(file.mtime)}
+              </span>
+              <span className="flex justify-center">
+                {uploaded ? (
+                  <span className={`inline-flex items-center gap-1 px-2.5 py-0.5 rounded text-[10px] font-semibold uppercase tracking-wide border ${badge.bg}`}>
+                    <CheckIcon className="w-3 h-3" />
+                    {badge.label}
+                  </span>
+                ) : (
+                  <span className={`inline-flex items-center gap-1 px-2.5 py-0.5 rounded text-[10px] font-semibold uppercase tracking-wide border ${badge.bg}`}>
+                    <UploadIcon className="w-3 h-3" />
+                    {badge.label}
+                  </span>
+                )}
+              </span>
+            </div>
+          );
+        })}
+      </div>
+    </div>
+  );
+}
+
+function FileSortHeader({
+  label,
+  sortKey,
+  currentKey,
+  dir,
+  onSort,
+  className = "",
+}: {
+  label: string;
+  sortKey: FileSortKey;
+  currentKey: FileSortKey;
+  dir: FileSortDir;
+  onSort: (key: FileSortKey) => void;
+  className?: string;
+}) {
+  const active = sortKey === currentKey;
+  const arrow = active ? (dir === "asc" ? " \u2191" : " \u2193") : "";
+  return (
+    <button
+      type="button"
+      onClick={() => onSort(sortKey)}
+      className={`flex items-center gap-1 hover:text-gray-700 cursor-pointer select-none ${active ? "text-gray-700" : ""} ${className}`}
+    >
+      {label}
+      {arrow && <span className="text-nlr-blue">{arrow}</span>}
+    </button>
+  );
+}

From b13abdf70c91b388cc97aeefe26af14f9b248647 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:33:37 -0700
Subject: [PATCH 078/173] Frontend: Add UnifiedFileTable component

---
 .../components/upload/UnifiedFileTable.tsx    | 449 ++++++++++++++++++
 1 file changed, 449 insertions(+)
 create mode 100644 frontend/src/components/upload/UnifiedFileTable.tsx

diff --git a/frontend/src/components/upload/UnifiedFileTable.tsx b/frontend/src/components/upload/UnifiedFileTable.tsx
new file mode 100644
index 0000000..1f5f65f
--- /dev/null
+++ b/frontend/src/components/upload/UnifiedFileTable.tsx
@@ -0,0 +1,449 @@
+/**
+ * Unified file table that persists across Review / Upload / Summary phases.
+ *
+ * Fixed 6-column grid — column content adapts per phase, but layout is stable.
+ * Uses @tanstack/react-virtual for 20K+ file handling.
+ */
+
+import { memo, useCallback, useEffect, useRef } from "react";
+import { useVirtualizer } from "@tanstack/react-virtual";
+
+import { formatBytes } from "../../utils/format/bytes.ts";
+import { formatDate } from "../../utils/format/date.ts";
+import type {
+  SortDir,
+  SortKey,
+  UnifiedFileRow,
+  UnifiedStatus,
+  UploadPhase,
+} from "../../types/upload.ts";
+// ── Grid template (fixed across all phases) ──
+
+const GRID_COLS = "grid-cols-[36px_1fr_1fr_80px_120px_1fr]";
+const ROW_HEIGHT = 40;
+
+// ── Props ──
+
+interface UnifiedFileTableProps {
+  phase: UploadPhase;
+  files: UnifiedFileRow[];
+  sortKey: SortKey;
+  sortDir: SortDir;
+  onSort: (key: SortKey) => void;
+  isSortFrozen: boolean;
+
+  // Selection (review phase only)
+  selectedPaths: Set<string>;
+  onToggleFile: (path: string) => void;
+  onToggleAllFiltered: () => void;
+  headerChecked: boolean;
+  headerIndeterminate: boolean;
+}
+
+export default function UnifiedFileTable({
+  phase,
+  files,
+  sortKey,
+  sortDir,
+  onSort,
+  isSortFrozen,
+  selectedPaths,
+  onToggleFile,
+  onToggleAllFiltered,
+  headerChecked,
+  headerIndeterminate,
+}: UnifiedFileTableProps) {
+  const scrollContainerRef = useRef<HTMLDivElement>(null);
+
+  const rowVirtualizer = useVirtualizer({
+    count: files.length,
+    getScrollElement: () => scrollContainerRef.current,
+    estimateSize: () => ROW_HEIGHT,
+    overscan: 20,
+  });
+
+  // Reset scroll when files change significantly (e.g., filter change)
+  const prevCountRef = useRef(files.length);
+  useEffect(() => {
+    if (Math.abs(files.length - prevCountRef.current) > 100) {
+      rowVirtualizer.scrollToIndex(0);
+    }
+    prevCountRef.current = files.length;
+  }, [files.length, rowVirtualizer]);
+
+  const scrollToActive = useCallback(() => {
+    const idx = files.findIndex(
+      (f) => f.status === "in_progress",
+    );
+    if (idx >= 0) {
+      rowVirtualizer.scrollToIndex(idx, { align: "center" });
+    }
+  }, [files, rowVirtualizer]);
+
+  // Count active files for the "jump to active" button
+  const hasActiveFiles = phase === "uploading" && files.some((f) => f.status === "in_progress");
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200 overflow-hidden relative">
+      {/* Header */}
+      <div
+        className={`grid ${GRID_COLS} gap-2 px-4 py-2 bg-gray-50 border-b border-gray-200 text-xs font-medium text-gray-500 uppercase tracking-wider`}
+      >
+        {/* Col 1: Checkbox / Status icon */}
+        <div className="flex items-center justify-center">
+          {phase === "review" ? (
+            <IndeterminateCheckbox
+              checked={headerChecked}
+              indeterminate={headerIndeterminate}
+              onChange={onToggleAllFiltered}
+            />
+          ) : (
+            <span />
+          )}
+        </div>
+
+        {/* Col 2: Filename */}
+        <SortHeader
+          label="Filename"
+          sortKey="filename"
+          currentKey={sortKey}
+          dir={sortDir}
+          onSort={onSort}
+          disabled={isSortFrozen}
+        />
+
+        {/* Col 3: Folder */}
+        <SortHeader
+          label="Folder"
+          sortKey="folder"
+          currentKey={sortKey}
+          dir={sortDir}
+          onSort={onSort}
+          disabled={isSortFrozen}
+        />
+
+        {/* Col 4: Size */}
+        <SortHeader
+          label="Size"
+          sortKey="size"
+          currentKey={sortKey}
+          dir={sortDir}
+          onSort={onSort}
+          disabled={isSortFrozen}
+          className="justify-end"
+        />
+
+        {/* Col 5: Status */}
+        <SortHeader
+          label="Status"
+          sortKey="status"
+          currentKey={sortKey}
+          dir={sortDir}
+          onSort={onSort}
+          disabled={isSortFrozen}
+          className="justify-center"
+        />
+
+        {/* Col 6: Detail (context-dependent) */}
+        <div>
+          {phase === "review" && "Modified"}
+          {phase === "uploading" && ""}
+          {phase === "summary" && "S3 Path"}
+        </div>
+      </div>
+
+      {/* Virtualized rows */}
+      {files.length === 0 ? (
+        <div className="p-6 text-center text-gray-400 text-sm">
+          No files match the current filter.
+        </div>
+      ) : (
+        <div
+          ref={scrollContainerRef}
+          className="overflow-auto"
+          style={{ height: Math.min(files.length * ROW_HEIGHT, 520) }}
+        >
+          <div
+            style={{
+              height: `${rowVirtualizer.getTotalSize()}px`,
+              width: "100%",
+              position: "relative",
+            }}
+          >
+            {rowVirtualizer.getVirtualItems().map((virtualRow) => {
+              const file = files[virtualRow.index]!;
+              return (
+                <FileRow
+                  key={file.path}
+                  row={file}
+                  phase={phase}
+                  isSelected={selectedPaths.has(file.path)}
+                  onToggle={onToggleFile}
+                  style={{
+                    position: "absolute",
+                    top: 0,
+                    left: 0,
+                    width: "100%",
+                    height: `${virtualRow.size}px`,
+                    transform: `translateY(${virtualRow.start}px)`,
+                  }}
+                />
+              );
+            })}
+          </div>
+        </div>
+      )}
+
+      {/* Footer */}
+      <div className="px-4 py-2 bg-gray-50 border-t border-gray-200 text-xs text-gray-500">
+        {files.length.toLocaleString()} file{files.length !== 1 ? "s" : ""}
+      </div>
+
+      {/* Jump to active button (upload phase only) */}
+      {hasActiveFiles && (
+        <button
+          type="button"
+          onClick={scrollToActive}
+          className="absolute bottom-12 right-4 px-3 py-1.5 text-xs font-medium
+            bg-nlr-blue text-white rounded-full shadow-lg hover:bg-blue-700
+            transition-colors z-10"
+        >
+          Jump to active
+        </button>
+      )}
+    </div>
+  );
+}
+
+// ── Row component (memoized — new object ref on mutation triggers re-render) ──
+
+interface FileRowProps {
+  row: UnifiedFileRow;
+  phase: UploadPhase;
+  isSelected: boolean;
+  onToggle: (path: string) => void;
+  style: React.CSSProperties;
+}
+
+const FileRow = memo(function FileRow({
+  row,
+  phase,
+  isSelected,
+  onToggle,
+  style,
+}: FileRowProps) {
+  return (
+    <div
+      className={`grid ${GRID_COLS} gap-2 px-4 items-center text-xs border-b border-gray-50 hover:bg-gray-50/50`}
+      style={style}
+    >
+      {/* Col 1: Checkbox / Status icon */}
+      <div className="flex items-center justify-center">
+        {phase === "review" ? (
+          <input
+            type="checkbox"
+            checked={isSelected}
+            onChange={() => onToggle(row.path)}
+            className="h-3.5 w-3.5 rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue cursor-pointer"
+          />
+        ) : (
+          <StatusIcon status={row.status} />
+        )}
+      </div>
+
+      {/* Col 2: Filename */}
+      <span className="text-gray-700 truncate" title={row.filename}>
+        {row.filename}
+      </span>
+
+      {/* Col 3: Folder */}
+      <span className="text-gray-500 truncate" title={row.folder}>
+        {row.folder}
+      </span>
+
+      {/* Col 4: Size */}
+      <span className="text-gray-500 text-right tabular-nums">
+        {formatBytes(row.size)}
+      </span>
+
+      {/* Col 5: Status */}
+      <div className="flex justify-center">
+        <StatusBadge status={row.status} progressPercent={row.progressPercent} phase={phase} />
+      </div>
+
+      {/* Col 6: Detail */}
+      <div className="text-gray-400 truncate">
+        {phase === "review" && formatDate(row.mtime)}
+        {phase === "uploading" && row.status === "in_progress" && (
+          <MiniProgressBar percent={row.progressPercent} />
+        )}
+        {phase === "summary" && (
+          <span title={row.s3Path}>{row.s3Path}</span>
+        )}
+      </div>
+    </div>
+  );
+});
+
+// ── Sub-components ──
+
+function StatusIcon({ status }: { status: UnifiedStatus }) {
+  switch (status) {
+    case "in_progress":
+      return (
+        <svg className="w-4 h-4 text-nlr-blue spinner" viewBox="0 0 24 24" fill="none">
+          <circle className="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" strokeWidth="4" />
+          <path className="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4z" />
+        </svg>
+      );
+    case "completed":
+      return (
+        <svg className="w-4 h-4 text-green-500" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+          <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2.5} d="M5 13l4 4L19 7" />
+        </svg>
+      );
+    case "failed":
+      return (
+        <svg className="w-4 h-4 text-red-500" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+          <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2.5} d="M6 18L18 6M6 6l12 12" />
+        </svg>
+      );
+    case "skipped":
+      return (
+        <svg className="w-4 h-4 text-yellow-500" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+          <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2.5} d="M5 12h14" />
+        </svg>
+      );
+    default:
+      // queued, new, already_uploaded
+      return <span className="w-4 h-4 rounded-full border-2 border-gray-300 block" />;
+  }
+}
+
+function StatusBadge({
+  status,
+  progressPercent,
+  phase,
+}: {
+  status: UnifiedStatus;
+  progressPercent: number;
+  phase: UploadPhase;
+}) {
+  // Review phase: show "new" or "uploaded" based on status
+  if (phase === "review") {
+    if (status === "already_uploaded") {
+      return (
+        <span className="px-2 py-0.5 rounded-full text-[10px] font-medium bg-yellow-100 text-yellow-700 transition-colors duration-300">
+          uploaded
+        </span>
+      );
+    }
+    return (
+      <span className="px-2 py-0.5 rounded-full text-[10px] font-medium bg-green-100 text-green-700 transition-colors duration-300">
+        new
+      </span>
+    );
+  }
+
+  // Upload / Summary phase
+  const styles: Record<string, string> = {
+    queued: "bg-gray-100 text-gray-500",
+    in_progress: "bg-blue-100 text-nlr-blue",
+    completed: "bg-green-100 text-green-700",
+    skipped: "bg-yellow-100 text-yellow-700",
+    failed: "bg-red-100 text-red-700",
+  };
+
+  const labels: Record<string, string> = {
+    queued: "queued",
+    in_progress: `${Math.round(progressPercent)}%`,
+    completed: "uploaded",
+    skipped: "skipped",
+    failed: "failed",
+  };
+
+  return (
+    <span
+      className={`px-2 py-0.5 rounded-full text-[10px] font-medium transition-colors duration-300 ${styles[status] ?? "bg-gray-100 text-gray-500"}`}
+    >
+      {labels[status] ?? status}
+    </span>
+  );
+}
+
+function MiniProgressBar({ percent }: { percent: number }) {
+  return (
+    <div className="w-full bg-gray-200 rounded-full h-1.5">
+      <div
+        className="bg-nlr-blue h-full rounded-full transition-all duration-300"
+        style={{ width: `${Math.min(100, percent)}%` }}
+      />
+    </div>
+  );
+}
+
+// ── Sortable column header ──
+
+function SortHeader({
+  label,
+  sortKey,
+  currentKey,
+  dir,
+  onSort,
+  disabled = false,
+  className = "",
+}: {
+  label: string;
+  sortKey: SortKey;
+  currentKey: SortKey;
+  dir: SortDir;
+  onSort: (key: SortKey) => void;
+  disabled?: boolean;
+  className?: string;
+}) {
+  const active = sortKey === currentKey;
+  const arrow = active ? (dir === "asc" ? " \u2191" : " \u2193") : "";
+  return (
+    <button
+      type="button"
+      onClick={() => !disabled && onSort(sortKey)}
+      disabled={disabled}
+      className={`flex items-center gap-1 select-none
+        ${disabled ? "cursor-default text-gray-400" : "hover:text-gray-700 cursor-pointer"}
+        ${active && !disabled ? "text-gray-700" : ""}
+        ${className}`}
+    >
+      {label}
+      {arrow && <span className="text-nlr-blue">{arrow}</span>}
+    </button>
+  );
+}
+
+// ── Indeterminate checkbox ──
+
+function IndeterminateCheckbox({
+  checked,
+  indeterminate,
+  onChange,
+}: {
+  checked: boolean;
+  indeterminate: boolean;
+  onChange: () => void;
+}) {
+  const ref = useRef<HTMLInputElement>(null);
+  useEffect(() => {
+    if (ref.current) {
+      ref.current.indeterminate = indeterminate;
+    }
+  }, [indeterminate]);
+  return (
+    <input
+      ref={ref}
+      type="checkbox"
+      checked={checked}
+      onChange={onChange}
+      className="h-3.5 w-3.5 rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue cursor-pointer"
+    />
+  );
+}
+

From df475ec12bb9680664f2f0d6b62cdcf14d71cf3a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:34:08 -0700
Subject: [PATCH 079/173] Frontend: Add upload Stepper component

---
 frontend/src/components/upload/Stepper.tsx | 39 ++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 frontend/src/components/upload/Stepper.tsx

diff --git a/frontend/src/components/upload/Stepper.tsx b/frontend/src/components/upload/Stepper.tsx
new file mode 100644
index 0000000..778af15
--- /dev/null
+++ b/frontend/src/components/upload/Stepper.tsx
@@ -0,0 +1,39 @@
+/**
+ * 4-step progress indicator for the upload workflow.
+ * Wrapper around the unified Stepper component.
+ */
+
+import Stepper from "../common/Stepper.tsx";
+import type { UploadStep } from "../../stores/uploadStore.ts";
+
+const steps = [
+  { number: 1, label: "Select" },
+  { number: 2, label: "Review" },
+  { number: 3, label: "Upload" },
+  { number: 4, label: "Complete" },
+];
+
+interface UploadStepperProps {
+  currentStep: UploadStep;
+  onStepClick?: (step: UploadStep) => void;
+  /** When true, disables clicking back to earlier steps. */
+  isUploading?: boolean;
+}
+
+export default function UploadStepper({
+  currentStep,
+  onStepClick,
+  isUploading = false,
+}: UploadStepperProps) {
+  return (
+    <Stepper
+      steps={steps}
+      currentStep={currentStep}
+      onStepClick={onStepClick as ((step: number) => void) | undefined}
+      isOperating={isUploading}
+      maxClickableStep={2}
+      ariaLabel="Upload steps"
+      testIdPrefix="step"
+    />
+  );
+}

From e5919a2cd40ad7d72c8934ceea4dbfc811f9682b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:34:38 -0700
Subject: [PATCH 080/173] Frontend: Add ConfirmModal component

---
 .../src/components/upload/ConfirmModal.tsx    | 111 ++++++++++++++++++
 1 file changed, 111 insertions(+)
 create mode 100644 frontend/src/components/upload/ConfirmModal.tsx

diff --git a/frontend/src/components/upload/ConfirmModal.tsx b/frontend/src/components/upload/ConfirmModal.tsx
new file mode 100644
index 0000000..734356b
--- /dev/null
+++ b/frontend/src/components/upload/ConfirmModal.tsx
@@ -0,0 +1,111 @@
+/**
+ * Pre-upload confirmation modal.
+ *
+ * Shows file count and total size, with a "Force re-upload duplicates" toggle
+ * that dynamically updates the file count.
+ */
+
+import { useMemo, useState } from "react";
+
+import { formatBytes } from "../../utils/format/bytes.ts";
+import Modal from "../common/Modal.tsx";
+
+interface ConfirmModalProps {
+  isOpen: boolean;
+  onClose: () => void;
+  onConfirm: (skipDuplicates: boolean) => void;
+  totalFiles: number;
+  alreadyUploaded: number;
+  totalSize: number;
+}
+
+export default function ConfirmModal({
+  isOpen,
+  onClose,
+  onConfirm,
+  totalFiles,
+  alreadyUploaded,
+  totalSize,
+}: ConfirmModalProps) {
+  const [forceReupload, setForceReupload] = useState(false);
+
+  const filesToUpload = useMemo(
+    () => (forceReupload ? totalFiles : totalFiles - alreadyUploaded),
+    [forceReupload, totalFiles, alreadyUploaded],
+  );
+
+  function handleConfirm() {
+    onConfirm(!forceReupload); // skipDuplicates = NOT forceReupload
+    setForceReupload(false);
+  }
+
+  function handleClose() {
+    setForceReupload(false);
+    onClose();
+  }
+
+  return (
+    <Modal
+      isOpen={isOpen}
+      onClose={handleClose}
+      title="Confirm Upload"
+      footer={
+        <div className="flex gap-3">
+          <button
+            type="button"
+            onClick={handleClose}
+            className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
+          >
+            Cancel
+          </button>
+          <button
+            type="button"
+            onClick={handleConfirm}
+            disabled={filesToUpload === 0}
+            className="px-4 py-2 text-sm font-medium rounded transition-colors
+              bg-nlr-blue text-white hover:bg-blue-700
+              disabled:bg-gray-300 disabled:text-gray-500 disabled:cursor-not-allowed"
+          >
+            Upload {filesToUpload.toLocaleString()} File{filesToUpload !== 1 ? "s" : ""}
+          </button>
+        </div>
+      }
+    >
+      <div className="space-y-4">
+        <div className="grid grid-cols-2 gap-4 text-center">
+          <div>
+            <div className="text-2xl font-bold text-gray-900">
+              {filesToUpload.toLocaleString()}
+            </div>
+            <div className="text-xs text-gray-500 mt-0.5">Files to Upload</div>
+          </div>
+          <div>
+            <div className="text-2xl font-bold text-gray-900">
+              {formatBytes(totalSize)}
+            </div>
+            <div className="text-xs text-gray-500 mt-0.5">Total Size</div>
+          </div>
+        </div>
+
+        {alreadyUploaded > 0 && (
+          <>
+            <div className="text-sm text-yellow-700 bg-yellow-50 border border-yellow-200 rounded p-2.5">
+              {alreadyUploaded.toLocaleString()} file{alreadyUploaded !== 1 ? "s" : ""} already
+              exist in S3 and will be skipped.
+            </div>
+
+            <label className="flex items-center gap-2 text-sm text-gray-600 cursor-pointer">
+              <input
+                type="checkbox"
+                checked={forceReupload}
+                onChange={(e) => setForceReupload(e.target.checked)}
+                className="rounded border-gray-300"
+              />
+              Force re-upload duplicates
+            </label>
+          </>
+        )}
+      </div>
+    </Modal>
+  );
+}

From 04585f89573af76506cae4c58d9213d50c94909a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:39:17 -0700
Subject: [PATCH 081/173] Frontend: Add review toolbar component

---
 .../src/components/upload/ReviewToolbar.tsx   | 194 ++++++++++++++++++
 1 file changed, 194 insertions(+)
 create mode 100644 frontend/src/components/upload/ReviewToolbar.tsx

diff --git a/frontend/src/components/upload/ReviewToolbar.tsx b/frontend/src/components/upload/ReviewToolbar.tsx
new file mode 100644
index 0000000..dba346f
--- /dev/null
+++ b/frontend/src/components/upload/ReviewToolbar.tsx
@@ -0,0 +1,194 @@
+/**
+ * Filter/search/selection toolbar for the review phase.
+ *
+ * During upload and summary phases, a simpler status filter bar is shown
+ * instead (handled separately in UploadPage).
+ */
+
+import { useState } from "react";
+
+import type { StatusFilter } from "../../types/upload.ts";
+
+interface ReviewToolbarProps {
+  statusFilter: StatusFilter;
+  onStatusFilterChange: (f: StatusFilter) => void;
+  searchQuery: string;
+  onSearchChange: (q: string) => void;
+  selectedCount: number;
+  totalCount: number;
+  filteredCount: number;
+  showFilteredCount: boolean;
+
+  // Selection actions
+  onSelectAll: () => void;
+  onSelectNewOnly: () => void;
+  onToggleAllFiltered: () => void;
+  onDeselectAll: () => void;
+  onSelectFirstN: (n: number) => void;
+  headerChecked: boolean;
+}
+
+export default function ReviewToolbar({
+  statusFilter,
+  onStatusFilterChange,
+  searchQuery,
+  onSearchChange,
+  selectedCount,
+  totalCount,
+  filteredCount,
+  showFilteredCount,
+  onSelectAll,
+  onSelectNewOnly,
+  onToggleAllFiltered,
+  onDeselectAll,
+  onSelectFirstN,
+  headerChecked,
+}: ReviewToolbarProps) {
+  const [selectFirstNInput, setSelectFirstNInput] = useState("");
+
+  const handleSelectFirstN = () => {
+    const n = Number.parseInt(selectFirstNInput, 10);
+    if (Number.isNaN(n) || n <= 0) return;
+    onSelectFirstN(n);
+    setSelectFirstNInput("");
+  };
+
+  return (
+    <div className="space-y-2">
+      {/* Row 1: Filters + count */}
+      <div className="flex items-center justify-between text-sm flex-wrap gap-2">
+        <div className="flex items-center gap-3">
+          <div className="flex items-center gap-2">
+            <label htmlFor="status-filter" className="text-gray-600">
+              Status:
+            </label>
+            <select
+              id="status-filter"
+              value={statusFilter}
+              onChange={(e) => onStatusFilterChange(e.target.value as StatusFilter)}
+              className="border border-gray-300 rounded px-2 py-1 text-sm bg-white"
+            >
+              <option value="all">All</option>
+              <option value="new">Not Uploaded</option>
+              <option value="uploaded">Already Uploaded</option>
+            </select>
+          </div>
+          <input
+            type="text"
+            value={searchQuery}
+            onChange={(e) => onSearchChange(e.target.value)}
+            placeholder="Search files..."
+            className="border border-gray-300 rounded px-2 py-1 text-sm bg-white w-48"
+          />
+        </div>
+        <div className="flex items-center gap-3 text-gray-500 text-sm">
+          <span className="text-nlr-blue font-medium">
+            {selectedCount.toLocaleString()} of {totalCount.toLocaleString()} selected
+          </span>
+          {showFilteredCount && (
+            <span>({filteredCount.toLocaleString()} shown)</span>
+          )}
+        </div>
+      </div>
+
+      {/* Row 2: Selection actions */}
+      <div className="flex items-center gap-4 text-xs flex-wrap">
+        <div className="flex items-center gap-1.5">
+          <span className="text-gray-400">Select:</span>
+          <button type="button" onClick={onSelectAll} className="text-nlr-blue hover:underline">
+            All
+          </button>
+          <span className="text-gray-300">|</span>
+          <button type="button" onClick={onSelectNewOnly} className="text-nlr-blue hover:underline">
+            Not Uploaded
+          </button>
+          <span className="text-gray-300">|</span>
+          <button type="button" onClick={onToggleAllFiltered} className="text-nlr-blue hover:underline">
+            {headerChecked ? "Deselect" : "Select"} Shown
+          </button>
+          <span className="text-gray-300">|</span>
+          <button type="button" onClick={onDeselectAll} className="text-nlr-blue hover:underline">
+            None
+          </button>
+        </div>
+        <div className="flex items-center gap-1.5">
+          <span className="text-gray-400">Select first</span>
+          <input
+            type="number"
+            min="1"
+            value={selectFirstNInput}
+            onChange={(e) => setSelectFirstNInput(e.target.value)}
+            onKeyDown={(e) => { if (e.key === "Enter") handleSelectFirstN(); }}
+            placeholder="#"
+            className="border border-gray-300 rounded px-1.5 py-0.5 text-xs bg-white w-16 tabular-nums"
+          />
+          <button
+            type="button"
+            onClick={handleSelectFirstN}
+            disabled={!selectFirstNInput || Number.parseInt(selectFirstNInput, 10) <= 0}
+            className="text-nlr-blue hover:underline disabled:text-gray-300 disabled:no-underline"
+          >
+            Go
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+}
+
+/**
+ * Simplified status filter for upload/summary phases.
+ * Shows a dropdown to filter by upload status.
+ */
+export function StatusFilterBar({
+  filter,
+  onFilterChange,
+  totalCount,
+  filteredCount,
+  searchQuery,
+  onSearchChange,
+}: {
+  filter: StatusFilter;
+  onFilterChange: (f: StatusFilter) => void;
+  totalCount: number;
+  filteredCount: number;
+  searchQuery: string;
+  onSearchChange: (q: string) => void;
+}) {
+  return (
+    <div className="flex items-center justify-between text-sm flex-wrap gap-2">
+      <div className="flex items-center gap-3">
+        <div className="flex items-center gap-2">
+          <label htmlFor="upload-status-filter" className="text-gray-600">
+            Show:
+          </label>
+          <select
+            id="upload-status-filter"
+            value={filter}
+            onChange={(e) => onFilterChange(e.target.value as StatusFilter)}
+            className="border border-gray-300 rounded px-2 py-1 text-sm bg-white"
+          >
+            <option value="all">All Files</option>
+            <option value="in_progress">In Progress</option>
+            <option value="completed">Uploaded</option>
+            <option value="skipped">Skipped</option>
+            <option value="failed">Failed</option>
+            <option value="queued">Queued</option>
+          </select>
+        </div>
+        <input
+          type="text"
+          value={searchQuery}
+          onChange={(e) => onSearchChange(e.target.value)}
+          placeholder="Search files..."
+          className="border border-gray-300 rounded px-2 py-1 text-sm bg-white w-48"
+        />
+      </div>
+      {filteredCount !== totalCount && (
+        <span className="text-gray-500 text-sm">
+          {filteredCount.toLocaleString()} of {totalCount.toLocaleString()} shown
+        </span>
+      )}
+    </div>
+  );
+}

From dce194b44190be344cf9297e29d3b10db94300b4 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:45:50 -0700
Subject: [PATCH 082/173] Frontend: Add icons for cloud and close/open

---
 frontend/src/utils/icons.tsx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
index 7fcfeec..6ca0e21 100644
--- a/frontend/src/utils/icons.tsx
+++ b/frontend/src/utils/icons.tsx
@@ -27,6 +27,9 @@ import {
   XCircle,
   Loader2,
   Plus,
+  Minus,
+  Cloud,
+  Circle,
   type LucideProps,
 } from "lucide-react";
 
@@ -54,6 +57,9 @@ export const RefreshIcon = RefreshCw;
 export const XCircleIcon = XCircle;
 export const SpinnerIcon = Loader2;
 export const PlusIcon = Plus;
+export const MinusIcon = Minus;
+export const CloudIcon = Cloud;
+export const CircleIcon = Circle;
 
 // Export type for icon props
 export type { LucideProps as IconProps };

From b680d6f8b7b3ad431e4734117279508dd1e1a98a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:46:29 -0700
Subject: [PATCH 083/173] Frontend: Use lucide progress icons

---
 .../components/upload/UnifiedFileTable.tsx    | 28 ++++---------------
 1 file changed, 6 insertions(+), 22 deletions(-)

diff --git a/frontend/src/components/upload/UnifiedFileTable.tsx b/frontend/src/components/upload/UnifiedFileTable.tsx
index 1f5f65f..ccf10fb 100644
--- a/frontend/src/components/upload/UnifiedFileTable.tsx
+++ b/frontend/src/components/upload/UnifiedFileTable.tsx
@@ -10,6 +10,7 @@ import { useVirtualizer } from "@tanstack/react-virtual";
 
 import { formatBytes } from "../../utils/format/bytes.ts";
 import { formatDate } from "../../utils/format/date.ts";
+import { SpinnerIcon, CheckIcon, XIcon, MinusIcon, CircleIcon } from "../../utils/icons.tsx";
 import type {
   SortDir,
   SortKey,
@@ -290,33 +291,16 @@ const FileRow = memo(function FileRow({
 function StatusIcon({ status }: { status: UnifiedStatus }) {
   switch (status) {
     case "in_progress":
-      return (
-        <svg className="w-4 h-4 text-nlr-blue spinner" viewBox="0 0 24 24" fill="none">
-          <circle className="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" strokeWidth="4" />
-          <path className="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4z" />
-        </svg>
-      );
+      return <SpinnerIcon className="w-4 h-4 text-nlr-blue animate-spin" />;
     case "completed":
-      return (
-        <svg className="w-4 h-4 text-green-500" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-          <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2.5} d="M5 13l4 4L19 7" />
-        </svg>
-      );
+      return <CheckIcon className="w-4 h-4 text-green-500" strokeWidth={2.5} />;
     case "failed":
-      return (
-        <svg className="w-4 h-4 text-red-500" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-          <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2.5} d="M6 18L18 6M6 6l12 12" />
-        </svg>
-      );
+      return <XIcon className="w-4 h-4 text-red-500" strokeWidth={2.5} />;
     case "skipped":
-      return (
-        <svg className="w-4 h-4 text-yellow-500" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-          <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2.5} d="M5 12h14" />
-        </svg>
-      );
+      return <MinusIcon className="w-4 h-4 text-yellow-500" strokeWidth={2.5} />;
     default:
       // queued, new, already_uploaded
-      return <span className="w-4 h-4 rounded-full border-2 border-gray-300 block" />;
+      return <CircleIcon className="w-4 h-4 text-gray-300" strokeWidth={2} />;
   }
 }
 

From 5bea536cdd64fb2c6118da13ad86ac7faf78e797 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:46:57 -0700
Subject: [PATCH 084/173] Frontend: Add lucide cloud icon

---
 frontend/src/components/files/S3Browser.tsx | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/frontend/src/components/files/S3Browser.tsx b/frontend/src/components/files/S3Browser.tsx
index d20d46d..ad96eea 100644
--- a/frontend/src/components/files/S3Browser.tsx
+++ b/frontend/src/components/files/S3Browser.tsx
@@ -1,6 +1,7 @@
 import { useCallback, useEffect, useState } from "react";
 import { apiGet } from "../../api/client.ts";
 import type { S3File, S3Folder, S3ListResponse } from "../../types/api.ts";
+import { CloudIcon } from "../../utils/icons.tsx";
 import Breadcrumb from "../common/Breadcrumb.tsx";
 import Spinner from "../common/Spinner.tsx";
 import FileList from "./FileList.tsx";
@@ -74,19 +75,7 @@ export default function S3Browser({ bucketName, region }: S3BrowserProps) {
       {/* Header: Bucket info + breadcrumb */}
       <div className="p-4 border-b border-gray-200">
         <div className="flex items-center gap-2 mb-2">
-          <svg
-            className="h-5 w-5 text-nlr-blue"
-            fill="none"
-            viewBox="0 0 24 24"
-            stroke="currentColor"
-          >
-            <path
-              strokeLinecap="round"
-              strokeLinejoin="round"
-              strokeWidth={2}
-              d="M3 15a4 4 0 004 4h9a5 5 0 10-.1-9.999 5.002 5.002 0 10-9.78 2.096A4.001 4.001 0 003 15z"
-            />
-          </svg>
+          <CloudIcon className="h-5 w-5 text-nlr-blue" />
           <span className="text-sm text-gray-500">
             {bucketName}
             <span className="ml-2 text-xs text-gray-400">({region})</span>

From 13b8b66e1e5bba20aacadd08ae5ac08f3560ca97 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:47:28 -0700
Subject: [PATCH 085/173] Frontend: Add Upload footer and header components

---
 .../src/components/upload/UploadFooter.tsx    | 103 ++++++
 .../src/components/upload/UploadHeader.tsx    | 300 ++++++++++++++++++
 2 files changed, 403 insertions(+)
 create mode 100644 frontend/src/components/upload/UploadFooter.tsx
 create mode 100644 frontend/src/components/upload/UploadHeader.tsx

diff --git a/frontend/src/components/upload/UploadFooter.tsx b/frontend/src/components/upload/UploadFooter.tsx
new file mode 100644
index 0000000..d39c786
--- /dev/null
+++ b/frontend/src/components/upload/UploadFooter.tsx
@@ -0,0 +1,103 @@
+/**
+ * Phase-aware footer with action buttons below the unified file table.
+ *
+ * - Review: Back + Start Upload
+ * - Upload: Cancel Upload
+ * - Summary: Download CSV + Upload More
+ */
+
+import type { UploadPhase } from "../../types/upload.ts";
+import { ChevronRightIcon, XCircleIcon, DownloadIcon, UploadIcon } from "../../utils/icons.tsx";
+
+interface UploadFooterProps {
+  phase: UploadPhase;
+
+  // Review
+  onBack?: () => void;
+  onStartUpload?: () => void;
+  selectedNewCount?: number;
+
+  // Upload
+  onCancel?: () => void;
+  isRunning?: boolean;
+
+  // Summary
+  onDownloadCsv?: () => void;
+  onUploadMore?: () => void;
+  failedCount?: number;
+}
+
+export default function UploadFooter({
+  phase,
+  onBack,
+  onStartUpload,
+  selectedNewCount = 0,
+  onCancel,
+  isRunning = false,
+  onDownloadCsv,
+  onUploadMore,
+}: UploadFooterProps) {
+  if (phase === "review") {
+    return (
+      <div className="flex items-center justify-between">
+        <button
+          type="button"
+          onClick={onBack}
+          className="px-4 py-2 text-sm font-medium text-gray-600 hover:text-gray-800 border border-gray-300 rounded hover:bg-gray-50"
+        >
+          Back
+        </button>
+        <button
+          type="button"
+          onClick={onStartUpload}
+          disabled={selectedNewCount === 0}
+          className="px-6 py-2 text-sm font-medium rounded transition-colors
+            bg-nlr-blue text-white hover:bg-blue-700
+            disabled:bg-gray-300 disabled:text-gray-500 disabled:cursor-not-allowed"
+        >
+          Start Upload ({selectedNewCount.toLocaleString()} file{selectedNewCount !== 1 ? "s" : ""})
+          <ChevronRightIcon className="w-4 h-4 ml-1 inline-block" strokeWidth={2.5} />
+        </button>
+      </div>
+    );
+  }
+
+  if (phase === "uploading") {
+    return (
+      <div className="flex justify-center pt-2">
+        {isRunning && (
+          <button
+            type="button"
+            onClick={onCancel}
+            className="px-6 py-2 text-sm font-medium text-red-600 border border-red-300 rounded hover:bg-red-50 transition-colors"
+          >
+            <XCircleIcon className="w-4 h-4 mr-1 inline-block" />
+            Cancel Upload
+          </button>
+        )}
+      </div>
+    );
+  }
+
+  // Summary
+  return (
+    <div className="flex items-center justify-center gap-4 pt-2">
+      <button
+        type="button"
+        onClick={onDownloadCsv}
+        className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
+      >
+        <DownloadIcon className="w-4 h-4 mr-1 inline-block" />
+        Download CSV
+      </button>
+      <button
+        type="button"
+        onClick={onUploadMore}
+        className="px-6 py-2 text-sm font-medium rounded transition-colors bg-nlr-blue text-white hover:bg-blue-700"
+      >
+        <UploadIcon className="w-4 h-4 mr-1 inline-block" />
+        Upload More
+      </button>
+    </div>
+  );
+}
diff --git a/frontend/src/components/upload/UploadHeader.tsx b/frontend/src/components/upload/UploadHeader.tsx
new file mode 100644
index 0000000..1c35a7d
--- /dev/null
+++ b/frontend/src/components/upload/UploadHeader.tsx
@@ -0,0 +1,300 @@
+/**
+ * Phase-aware header that sits above the unified file table.
+ *
+ * - Review: stat cards + scanning indicator
+ * - Upload: progress bar + counters + ETA
+ * - Summary: summary stat cards + job status headline
+ *
+ * Uses crossfade transitions between phases.
+ */
+
+import type { UploadJob } from "../../types/api.ts";
+import type { StatusFilter, UploadPhase } from "../../types/upload.ts";
+import { formatBytes } from "../../utils/format/bytes.ts";
+import { formatSpeed } from "../../utils/format/speed.ts";
+import { formatDuration, formatEta } from "../../utils/format/time.ts";
+import ProgressBar from "../common/ProgressBar.tsx";
+import Spinner from "../common/Spinner.tsx";
+import StatCard from "../common/StatCard.tsx";
+import { WarningIcon } from "../../utils/icons.tsx";
+
+interface UploadHeaderProps {
+  phase: UploadPhase;
+
+  // Review data
+  totals: { totalFiles: number; alreadyUploaded: number; totalSize: number };
+  isScanning: boolean;
+  foldersFound: number;
+
+  // Upload data
+  progressPercent: number;
+  filesProcessed: number;
+  totalFiles: number;
+  statusCounts: { uploaded: number; skipped: number; failed: number };
+  eta: number | null;
+  isRunning: boolean;
+  uploadedBytesFormatted: string;
+  totalBytesFormatted: string;
+
+  // Summary data
+  job: UploadJob | null;
+
+  // Clickable status counters
+  onFilterClick?: (filter: StatusFilter) => void;
+}
+
+export default function UploadHeader({
+  phase,
+  totals,
+  isScanning,
+  foldersFound,
+  progressPercent,
+  filesProcessed,
+  totalFiles,
+  statusCounts,
+  eta,
+  isRunning,
+  uploadedBytesFormatted,
+  totalBytesFormatted,
+  job,
+  onFilterClick,
+}: UploadHeaderProps) {
+  if (phase === "review") {
+    return <ReviewHeader totals={totals} isScanning={isScanning} foldersFound={foldersFound} />;
+  }
+
+  if (phase === "uploading") {
+    return (
+      <UploadingHeader
+        progressPercent={progressPercent}
+        filesProcessed={filesProcessed}
+        totalFiles={totalFiles}
+        statusCounts={statusCounts}
+        eta={eta}
+        isRunning={isRunning}
+        uploadedBytesFormatted={uploadedBytesFormatted}
+        totalBytesFormatted={totalBytesFormatted}
+        onFilterClick={onFilterClick}
+      />
+    );
+  }
+
+  return <SummaryHeader job={job} onFilterClick={onFilterClick} />;
+}
+
+// ── Review phase ──
+
+function ReviewHeader({
+  totals,
+  isScanning,
+  foldersFound,
+}: {
+  totals: { totalFiles: number; alreadyUploaded: number; totalSize: number };
+  isScanning: boolean;
+  foldersFound: number;
+}) {
+  const newFiles = totals.totalFiles - totals.alreadyUploaded;
+  return (
+    <div className="space-y-3 animate-in fade-in duration-200">
+      <div className="grid grid-cols-2 sm:grid-cols-4 gap-3">
+        <StatCard value={totals.totalFiles.toLocaleString()} label="Total Files" color="text-nlr-blue" />
+        <StatCard value={formatBytes(totals.totalSize)} label="Total Size" color="text-nlr-blue" />
+        <StatCard value={totals.alreadyUploaded.toLocaleString()} label="Already Uploaded" color="text-yellow-500" />
+        <StatCard value={newFiles.toLocaleString()} label="New Files" color="text-green-600" />
+      </div>
+
+      {isScanning && (
+        <div className="flex items-center gap-3 p-3 bg-blue-50 rounded-lg border border-blue-200">
+          <Spinner size="sm" />
+          <span className="text-sm text-blue-700">
+            Scanning folders... ({foldersFound} folder{foldersFound !== 1 ? "s" : ""} found so far)
+          </span>
+        </div>
+      )}
+    </div>
+  );
+}
+
+// ── Upload phase ──
+
+function UploadingHeader({
+  progressPercent,
+  filesProcessed,
+  totalFiles,
+  statusCounts,
+  eta,
+  isRunning,
+  uploadedBytesFormatted,
+  totalBytesFormatted,
+  onFilterClick,
+}: {
+  progressPercent: number;
+  filesProcessed: number;
+  totalFiles: number;
+  statusCounts: { uploaded: number; skipped: number; failed: number };
+  eta: number | null;
+  isRunning: boolean;
+  uploadedBytesFormatted: string;
+  totalBytesFormatted: string;
+  onFilterClick?: (filter: StatusFilter) => void;
+}) {
+  return (
+    <div className="space-y-3 animate-in fade-in duration-200">
+      {/* Progress bar card */}
+      <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-4">
+        <div className="flex items-center justify-between mb-2">
+          <h3 className="text-sm font-semibold text-gray-900">
+            {isRunning ? "Uploading..." : "Upload Complete"}
+          </h3>
+          {isRunning && <Spinner size="sm" />}
+        </div>
+
+        <ProgressBar
+          percent={progressPercent}
+          label={`${filesProcessed} / ${totalFiles} files`}
+        />
+
+        <div className="flex items-center justify-between mt-2 text-xs text-gray-500">
+          <span>
+            {uploadedBytesFormatted || "0 B"} / {totalBytesFormatted || "0 B"}
+          </span>
+          <span>ETA: {formatEta(eta)}</span>
+        </div>
+      </div>
+
+      {/* Clickable status counters */}
+      <div className="grid grid-cols-3 gap-3">
+        <StatusCounterButton
+          count={statusCounts.uploaded}
+          label="Uploaded"
+          color="text-green-600"
+          bgColor="bg-green-50"
+          borderColor="border-green-200"
+          onClick={() => onFilterClick?.("completed")}
+        />
+        <StatusCounterButton
+          count={statusCounts.skipped}
+          label="Skipped"
+          color="text-yellow-600"
+          bgColor="bg-yellow-50"
+          borderColor="border-yellow-200"
+          onClick={() => onFilterClick?.("skipped")}
+        />
+        <StatusCounterButton
+          count={statusCounts.failed}
+          label="Failed"
+          color="text-red-600"
+          bgColor="bg-red-50"
+          borderColor="border-red-200"
+          onClick={() => onFilterClick?.("failed")}
+        />
+      </div>
+    </div>
+  );
+}
+
+// ── Summary phase ──
+
+function SummaryHeader({
+  job,
+  onFilterClick,
+}: {
+  job: UploadJob | null;
+  onFilterClick?: (filter: StatusFilter) => void;
+}) {
+  if (!job) return null;
+
+  const headlineColor = job.files_failed > 0
+    ? "text-yellow-600"
+    : job.cancelled
+      ? "text-gray-600"
+      : "text-green-600";
+
+  const headlineText = job.cancelled
+    ? "Upload Cancelled"
+    : job.files_failed > 0 && job.files_uploaded > 0
+      ? "Upload Partial Success"
+      : job.files_failed > 0
+        ? "Upload Failed"
+        : "Upload Complete";
+
+  return (
+    <div className="space-y-3 animate-in fade-in duration-200">
+      <div className="text-center">
+        <h3 className={`text-lg font-bold ${headlineColor}`}>{headlineText}</h3>
+      </div>
+
+      <div className="grid grid-cols-2 sm:grid-cols-3 lg:grid-cols-6 gap-3">
+        <button
+          type="button"
+          onClick={() => onFilterClick?.("completed")}
+          className="text-left"
+        >
+          <StatCard value={job.files_uploaded.toLocaleString()} label="Uploaded" color="text-green-600" />
+        </button>
+        <button
+          type="button"
+          onClick={() => onFilterClick?.("skipped")}
+          className="text-left"
+        >
+          <StatCard value={job.files_skipped.toLocaleString()} label="Skipped" color="text-yellow-500" />
+        </button>
+        <button
+          type="button"
+          onClick={() => onFilterClick?.("failed")}
+          className="text-left"
+        >
+          <StatCard value={job.files_failed.toLocaleString()} label="Failed" color="text-red-500" />
+        </button>
+        <StatCard value={job.successfully_uploaded_bytes_formatted} label="Data Uploaded" color="text-nlr-blue" />
+        <StatCard value={formatDuration(job.total_upload_duration_seconds)} label="Duration" color="text-nlr-blue" />
+        <StatCard value={formatSpeed(job.average_upload_speed_mbps)} label="Avg Speed" color="text-nlr-blue" />
+      </div>
+
+      {job.files_failed > 0 && (
+        <div className="flex items-center gap-2 p-3 bg-red-50 rounded-lg border border-red-200 text-sm text-red-700">
+          <WarningIcon className="w-4 h-4 flex-shrink-0" />
+          <span>
+            <strong>{job.files_failed}</strong> file{job.files_failed !== 1 ? "s" : ""} failed to upload.
+            <button
+              type="button"
+              onClick={() => onFilterClick?.("failed")}
+              className="ml-1 text-red-800 underline hover:no-underline"
+            >
+              Show failed files
+            </button>
+          </span>
+        </div>
+      )}
+    </div>
+  );
+}
+
+// ── Clickable status counter ──
+
+function StatusCounterButton({
+  count,
+  label,
+  color,
+  bgColor,
+  borderColor,
+  onClick,
+}: {
+  count: number;
+  label: string;
+  color: string;
+  bgColor: string;
+  borderColor: string;
+  onClick: () => void;
+}) {
+  return (
+    <button
+      type="button"
+      onClick={onClick}
+      className={`${bgColor} ${borderColor} border rounded-lg p-3 text-center hover:opacity-80 transition-opacity cursor-pointer`}
+    >
+      <div className={`text-xl font-bold ${color}`}>{count.toLocaleString()}</div>
+      <div className="text-xs text-gray-500 mt-0.5">{label}</div>
+    </button>
+  );
+}

From e8f8180be22c447da70d0931b92737febea2887b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:48:40 -0700
Subject: [PATCH 086/173] Frontend: Add DeleteStepper component

---
 .../src/components/delete/DeleteStepper.tsx   | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 frontend/src/components/delete/DeleteStepper.tsx

diff --git a/frontend/src/components/delete/DeleteStepper.tsx b/frontend/src/components/delete/DeleteStepper.tsx
new file mode 100644
index 0000000..56e53ed
--- /dev/null
+++ b/frontend/src/components/delete/DeleteStepper.tsx
@@ -0,0 +1,39 @@
+/**
+ * 5-step progress indicator for the delete workflow.
+ * Wrapper around the unified Stepper component.
+ */
+
+import Stepper from "../common/Stepper.tsx";
+import type { DeleteStep } from "../../stores/deleteStore.ts";
+
+const steps = [
+  { number: 1, label: "Select" },
+  { number: 2, label: "Review" },
+  { number: 3, label: "Confirm" },
+  { number: 4, label: "Clear" },
+  { number: 5, label: "Complete" },
+];
+
+interface DeleteStepperProps {
+  currentStep: DeleteStep;
+  onStepClick?: (step: DeleteStep) => void;
+  isDeleting?: boolean;
+}
+
+export default function DeleteStepper({
+  currentStep,
+  onStepClick,
+  isDeleting = false,
+}: DeleteStepperProps) {
+  return (
+    <Stepper
+      steps={steps}
+      currentStep={currentStep}
+      onStepClick={onStepClick as ((step: number) => void) | undefined}
+      isOperating={isDeleting}
+      maxClickableStep={2}
+      ariaLabel="Delete steps"
+      testIdPrefix="delete-step"
+    />
+  );
+}

From 6cc7b5d741860232755cf5d5ecd947c668febd37 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:49:00 -0700
Subject: [PATCH 087/173] Frontend: Add DeleteConfirmation component

---
 .../components/delete/DeleteConfirmation.tsx  | 110 ++++++++++++++++++
 1 file changed, 110 insertions(+)
 create mode 100644 frontend/src/components/delete/DeleteConfirmation.tsx

diff --git a/frontend/src/components/delete/DeleteConfirmation.tsx b/frontend/src/components/delete/DeleteConfirmation.tsx
new file mode 100644
index 0000000..a973ac2
--- /dev/null
+++ b/frontend/src/components/delete/DeleteConfirmation.tsx
@@ -0,0 +1,110 @@
+/**
+ * Confirmation step for the delete workflow (Step 3).
+ *
+ * Requires the user to type "DELETE" and check a confirmation checkbox
+ * before enabling the delete button. Emphasizes that S3 data is untouched.
+ */
+
+import { useState } from "react";
+
+import { formatBytes } from "../../utils/format/bytes.ts";
+import AlertBanner from "../common/AlertBanner.tsx";
+
+interface DeleteConfirmationProps {
+  totalFiles: number;
+  totalSize: number;
+  onConfirm: () => void;
+  onBack: () => void;
+}
+
+export default function DeleteConfirmation({
+  totalFiles,
+  totalSize,
+  onConfirm,
+  onBack,
+}: DeleteConfirmationProps) {
+  const [typedText, setTypedText] = useState("");
+  const [checked, setChecked] = useState(false);
+
+  const isConfirmed = typedText === "CLEAR" && checked;
+
+  return (
+    <div className="max-w-lg mx-auto space-y-6">
+      {/* Warning banner */}
+      <AlertBanner
+        type="error"
+        title="This action is irreversible"
+        message={
+          <>
+            You are about to permanently remove{" "}
+            <strong>{totalFiles} local file{totalFiles !== 1 ? "s" : ""}</strong>{" "}
+            ({formatBytes(totalSize)}) from this hard drive.
+          </>
+        }
+      />
+
+      {/* S3 reassurance */}
+      <AlertBanner
+        type="shield"
+        title="S3 data will NOT be affected"
+        message="Only local copies are deleted. Your files in S3 remain safe and unchanged. Each file is verified against S3 before deletion."
+      />
+
+      {/* Type-to-confirm */}
+      <div>
+        <label
+          htmlFor="delete-confirm-input"
+          className="block text-sm font-medium text-gray-700 mb-2"
+        >
+          Type <strong className="text-red-600">CLEAR</strong> to confirm
+        </label>
+        <input
+          id="delete-confirm-input"
+          type="text"
+          value={typedText}
+          onChange={(e) => setTypedText(e.target.value)}
+          className="w-full px-3 py-2 border border-gray-300 rounded-md text-sm focus:ring-2 focus:ring-red-500 focus:border-red-500"
+          placeholder="Type CLEAR here"
+          autoComplete="off"
+        />
+      </div>
+
+      {/* Checkbox */}
+      <label className="flex items-start gap-3 cursor-pointer">
+        <input
+          type="checkbox"
+          checked={checked}
+          onChange={(e) => setChecked(e.target.checked)}
+          className="mt-1 h-4 w-4 rounded border-gray-300 text-red-600 focus:ring-red-500"
+        />
+        <span className="text-sm text-gray-700">
+          I understand that cleared files cannot be recovered from this drive
+          and that the S3 copies have been verified.
+        </span>
+      </label>
+
+      {/* Buttons */}
+      <div className="flex gap-3">
+        <button
+          type="button"
+          onClick={onBack}
+          className="px-4 py-2 text-sm font-medium text-gray-700 bg-white border border-gray-300 rounded-md hover:bg-gray-50"
+        >
+          Back
+        </button>
+        <button
+          type="button"
+          onClick={onConfirm}
+          disabled={!isConfirmed}
+          className={`px-4 py-2 text-sm font-medium text-white rounded-md ${
+            isConfirmed
+              ? "bg-red-600 hover:bg-red-700"
+              : "bg-gray-300 cursor-not-allowed"
+          }`}
+        >
+          Clear {totalFiles} File{totalFiles !== 1 ? "s" : ""}
+        </button>
+      </div>
+    </div>
+  );
+}

From 8111e474ed40d33b622d01e35138fc0f64ba8671 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:50:07 -0700
Subject: [PATCH 088/173] Frontend: Add Settings components

---
 .../src/components/settings/CacheSection.tsx  | 106 +++++++
 .../src/components/settings/DangerZone.tsx    | 106 +++++++
 .../src/components/settings/SettingsForm.tsx  | 293 ++++++++++++++++++
 .../src/components/settings/UpdateSection.tsx | 143 +++++++++
 4 files changed, 648 insertions(+)
 create mode 100644 frontend/src/components/settings/CacheSection.tsx
 create mode 100644 frontend/src/components/settings/DangerZone.tsx
 create mode 100644 frontend/src/components/settings/SettingsForm.tsx
 create mode 100644 frontend/src/components/settings/UpdateSection.tsx

diff --git a/frontend/src/components/settings/CacheSection.tsx b/frontend/src/components/settings/CacheSection.tsx
new file mode 100644
index 0000000..15f490a
--- /dev/null
+++ b/frontend/src/components/settings/CacheSection.tsx
@@ -0,0 +1,106 @@
+import { useEffect, useState } from "react";
+import { apiGet, apiPost } from "../../api/client.ts";
+import { useAppStore } from "../../stores/appStore.ts";
+import type { CacheStats, CacheSyncResult } from "../../types/api.ts";
+
+export default function CacheSection() {
+  const { addNotification } = useAppStore();
+
+  const [stats, setStats] = useState<CacheStats | null>(null);
+  const [loading, setLoading] = useState(true);
+  const [syncing, setSyncing] = useState(false);
+  const [syncResult, setSyncResult] = useState<CacheSyncResult | null>(null);
+
+  async function loadStats() {
+    setLoading(true);
+    try {
+      const data = await apiGet<CacheStats>("/api/settings/cache/stats");
+      setStats(data);
+    } catch {
+      addNotification("error", "Failed to load cache statistics");
+    } finally {
+      setLoading(false);
+    }
+  }
+
+  useEffect(() => {
+    loadStats();
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, []);
+
+  async function handleSync() {
+    setSyncing(true);
+    setSyncResult(null);
+    try {
+      const result = await apiPost<CacheSyncResult>("/api/settings/cache/sync");
+      setSyncResult(result);
+      if (result.success) {
+        addNotification("success", "Cache synced with AWS");
+        loadStats();
+      } else {
+        addNotification("error", result.error ?? "Cache sync failed");
+      }
+    } catch {
+      addNotification("error", "Failed to sync cache");
+    } finally {
+      setSyncing(false);
+    }
+  }
+
+  return (
+    <div className="bg-white rounded-lg shadow p-6">
+      <h3 className="text-lg font-semibold text-nlr-text mb-4">Upload Cache</h3>
+
+      {loading ? (
+        <p className="text-sm text-gray-500">Loading cache statistics...</p>
+      ) : stats?.success ? (
+        <div className="grid grid-cols-2 sm:grid-cols-4 gap-4 mb-4">
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Total Entries</div>
+            <div className="text-lg font-semibold text-nlr-text mt-1">
+              {stats.stats.total_entries.toLocaleString()}
+            </div>
+          </div>
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Exists</div>
+            <div className="text-lg font-semibold text-nlr-green mt-1">
+              {stats.stats.exists_count.toLocaleString()}
+            </div>
+          </div>
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Not Exists</div>
+            <div className="text-lg font-semibold text-gray-500 mt-1">
+              {stats.stats.not_exists_count.toLocaleString()}
+            </div>
+          </div>
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Bucket</div>
+            <div className="text-sm font-mono text-nlr-text mt-1 truncate" title={stats.stats.bucket}>
+              {stats.stats.bucket || "-"}
+            </div>
+          </div>
+        </div>
+      ) : (
+        <p className="text-sm text-gray-500 mb-4">No cache data available.</p>
+      )}
+
+      {/* Sync result */}
+      {syncResult?.success && (
+        <div className="mb-4 p-3 rounded-md text-sm bg-green-50 text-green-800 border border-green-200">
+          Synced: {syncResult.files_in_s3?.toLocaleString()} files in S3,{" "}
+          {syncResult.files_updated?.toLocaleString()} updated,{" "}
+          {syncResult.files_removed?.toLocaleString()} removed
+        </div>
+      )}
+
+      <button
+        type="button"
+        onClick={handleSync}
+        disabled={syncing}
+        className="px-4 py-2 text-sm font-medium text-nlr-blue border border-nlr-blue rounded-md hover:bg-nlr-blue hover:text-white disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+      >
+        {syncing ? "Syncing..." : "Sync with AWS"}
+      </button>
+    </div>
+  );
+}
diff --git a/frontend/src/components/settings/DangerZone.tsx b/frontend/src/components/settings/DangerZone.tsx
new file mode 100644
index 0000000..8a5ba39
--- /dev/null
+++ b/frontend/src/components/settings/DangerZone.tsx
@@ -0,0 +1,106 @@
+import { useState } from "react";
+import { apiPost } from "../../api/client.ts";
+import { useAppStore } from "../../stores/appStore.ts";
+
+const DEFAULT_SETTINGS = {
+  aws_profile: "default",
+  aws_region: "us-west-2",
+  s3_bucket: "",
+  default_upload_folder: "",
+  display_name: "",
+  log_directory: "logs",
+};
+
+export default function DangerZone() {
+  const { updateSettings, addNotification } = useAppStore();
+
+  const [clearing, setClearing] = useState(false);
+  const [resetting, setResetting] = useState(false);
+
+  async function handleClearCache() {
+    if (!window.confirm("Are you sure you want to clear the upload cache? This cannot be undone.")) {
+      return;
+    }
+
+    setClearing(true);
+    try {
+      const result = await apiPost<{ success: boolean; deleted: number; message: string }>(
+        "/api/settings/cache/invalidate",
+      );
+      if (result.success) {
+        addNotification("success", `Cleared ${result.deleted} cache entries`);
+      } else {
+        addNotification("error", "Failed to clear cache");
+      }
+    } catch {
+      addNotification("error", "Failed to clear cache");
+    } finally {
+      setClearing(false);
+    }
+  }
+
+  async function handleResetSettings() {
+    if (
+      !window.confirm(
+        "Are you sure you want to reset all settings to defaults? This cannot be undone.",
+      )
+    ) {
+      return;
+    }
+
+    setResetting(true);
+    try {
+      await updateSettings(DEFAULT_SETTINGS);
+      addNotification("info", "Settings reset to defaults");
+    } catch {
+      addNotification("error", "Failed to reset settings");
+    } finally {
+      setResetting(false);
+    }
+  }
+
+  return (
+    <div className="bg-white rounded-lg shadow p-6 border-2 border-red-300">
+      <h3 className="text-lg font-semibold text-red-600 mb-2">Danger Zone</h3>
+      <p className="text-sm text-gray-500 mb-4">
+        These actions are destructive and cannot be undone.
+      </p>
+
+      <div className="space-y-3">
+        <div className="flex items-center justify-between p-3 rounded-md border border-red-200 bg-red-50/50">
+          <div>
+            <div className="text-sm font-medium text-nlr-text">Clear Upload Cache</div>
+            <div className="text-xs text-gray-500">
+              Removes all cached duplicate-check entries for the current bucket.
+            </div>
+          </div>
+          <button
+            type="button"
+            onClick={handleClearCache}
+            disabled={clearing}
+            className="ml-4 px-4 py-2 text-sm font-medium text-red-600 border border-red-300 rounded-md hover:bg-red-600 hover:text-white disabled:opacity-50 disabled:cursor-not-allowed transition-colors whitespace-nowrap"
+          >
+            {clearing ? "Clearing..." : "Clear Cache"}
+          </button>
+        </div>
+
+        <div className="flex items-center justify-between p-3 rounded-md border border-red-200 bg-red-50/50">
+          <div>
+            <div className="text-sm font-medium text-nlr-text">Reset Settings</div>
+            <div className="text-xs text-gray-500">
+              Restores all settings to their default values.
+            </div>
+          </div>
+          <button
+            type="button"
+            onClick={handleResetSettings}
+            disabled={resetting}
+            className="ml-4 px-4 py-2 text-sm font-medium text-red-600 border border-red-300 rounded-md hover:bg-red-600 hover:text-white disabled:opacity-50 disabled:cursor-not-allowed transition-colors whitespace-nowrap"
+          >
+            {resetting ? "Resetting..." : "Reset Settings"}
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+}
diff --git a/frontend/src/components/settings/SettingsForm.tsx b/frontend/src/components/settings/SettingsForm.tsx
new file mode 100644
index 0000000..5f74fc2
--- /dev/null
+++ b/frontend/src/components/settings/SettingsForm.tsx
@@ -0,0 +1,293 @@
+import { useEffect, useState } from "react";
+import { apiGet, apiPost } from "../../api/client.ts";
+import { useAppStore } from "../../stores/appStore.ts";
+import type { AppSettings, ConnectionTestResult } from "../../types/api.ts";
+
+const AWS_REGIONS = ["us-east-1", "us-east-2", "us-west-1", "us-west-2"];
+
+export default function SettingsForm() {
+  const { settings, updateSettings } = useAppStore();
+
+  const [profiles, setProfiles] = useState<string[]>([]);
+  const [formValues, setFormValues] = useState<Partial<AppSettings>>({});
+  const [isDirty, setIsDirty] = useState(false);
+  const [saving, setSaving] = useState(false);
+  const [customRegion, setCustomRegion] = useState(false);
+
+  // Connection test state
+  const [testing, setTesting] = useState(false);
+  const [testResult, setTestResult] = useState<ConnectionTestResult | null>(
+    null,
+  );
+
+  // Load profiles on mount
+  useEffect(() => {
+    apiGet<{ profiles: string[] }>("/api/settings/profiles")
+      .then((data) => setProfiles(data.profiles))
+      .catch(() => {
+        /* profiles are non-critical */
+      });
+  }, []);
+
+  // Sync form values when settings load
+  useEffect(() => {
+    if (settings) {
+      setFormValues({
+        aws_profile: settings.aws_profile,
+        aws_region: settings.aws_region,
+        s3_bucket: settings.s3_bucket,
+        default_upload_folder: settings.default_upload_folder,
+        display_name: settings.display_name,
+        log_directory: settings.log_directory,
+      });
+      // Check if the current region is not in our standard list
+      setCustomRegion(!AWS_REGIONS.includes(settings.aws_region));
+      setIsDirty(false);
+    }
+  }, [settings]);
+
+  function handleChange(field: keyof AppSettings, value: string) {
+    setFormValues((prev) => ({ ...prev, [field]: value }));
+    setIsDirty(true);
+    setTestResult(null);
+  }
+
+  function handleRegionSelect(value: string) {
+    if (value === "__other__") {
+      setCustomRegion(true);
+      handleChange("aws_region", "");
+    } else {
+      setCustomRegion(false);
+      handleChange("aws_region", value);
+    }
+  }
+
+  async function handleTestConnection() {
+    setTesting(true);
+    setTestResult(null);
+    try {
+      const result = await apiPost<ConnectionTestResult>(
+        "/api/settings/validate",
+        {
+          aws_profile: formValues.aws_profile,
+          aws_region: formValues.aws_region,
+          s3_bucket: formValues.s3_bucket,
+        },
+      );
+      setTestResult(result);
+    } catch {
+      setTestResult({ success: false, error: "Connection test failed" });
+    } finally {
+      setTesting(false);
+    }
+  }
+
+  async function handleSave() {
+    setSaving(true);
+    try {
+      await updateSettings(formValues);
+      setIsDirty(false);
+    } finally {
+      setSaving(false);
+    }
+  }
+
+  return (
+    <div className="bg-white rounded-lg shadow p-6">
+      <h3 className="text-lg font-semibold text-nlr-text mb-4">
+        AWS Configuration
+      </h3>
+
+      <div className="space-y-4">
+        {/* AWS Profile */}
+        <div>
+          <label
+            htmlFor="aws_profile"
+            className="block text-sm font-medium text-gray-700 mb-1"
+          >
+            AWS Profile
+          </label>
+          <select
+            id="aws_profile"
+            value={formValues.aws_profile ?? ""}
+            onChange={(e) => handleChange("aws_profile", e.target.value)}
+            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+          >
+            {profiles.map((p) => (
+              <option key={p} value={p}>
+                {p}
+              </option>
+            ))}
+            {/* If current profile is not in profiles list, show it anyway */}
+            {formValues.aws_profile &&
+              !profiles.includes(formValues.aws_profile) && (
+                <option value={formValues.aws_profile}>
+                  {formValues.aws_profile}
+                </option>
+              )}
+          </select>
+        </div>
+
+        {/* AWS Region */}
+        <div>
+          <label
+            htmlFor="aws_region"
+            className="block text-sm font-medium text-gray-700 mb-1"
+          >
+            AWS Region
+          </label>
+          {!customRegion ? (
+            <select
+              id="aws_region"
+              value={formValues.aws_region ?? ""}
+              onChange={(e) => handleRegionSelect(e.target.value)}
+              className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+            >
+              {AWS_REGIONS.map((r) => (
+                <option key={r} value={r}>
+                  {r}
+                </option>
+              ))}
+              <option value="__other__">Other...</option>
+            </select>
+          ) : (
+            <div className="flex gap-2">
+              <input
+                id="aws_region"
+                type="text"
+                value={formValues.aws_region ?? ""}
+                onChange={(e) => handleChange("aws_region", e.target.value)}
+                placeholder="e.g., eu-north-1"
+                className="flex-1 rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+              />
+              <button
+                type="button"
+                onClick={() => {
+                  setCustomRegion(false);
+                  handleChange("aws_region", AWS_REGIONS[0]);
+                }}
+                className="px-3 py-2 text-sm text-gray-600 hover:text-gray-800 border border-gray-300 rounded-md"
+              >
+                Standard
+              </button>
+            </div>
+          )}
+        </div>
+
+        {/* S3 Bucket */}
+        <div>
+          <label
+            htmlFor="s3_bucket"
+            className="block text-sm font-medium text-gray-700 mb-1"
+          >
+            S3 Bucket
+          </label>
+          <input
+            id="s3_bucket"
+            type="text"
+            value={formValues.s3_bucket ?? ""}
+            onChange={(e) => handleChange("s3_bucket", e.target.value)}
+            placeholder="my-bucket-name"
+            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+          />
+        </div>
+
+        {/* Default Upload Folder */}
+        <div>
+          <label
+            htmlFor="default_upload_folder"
+            className="block text-sm font-medium text-gray-700 mb-1"
+          >
+            Default Upload Folder
+          </label>
+          <input
+            id="default_upload_folder"
+            type="text"
+            value={formValues.default_upload_folder ?? ""}
+            onChange={(e) =>
+              handleChange("default_upload_folder", e.target.value)
+            }
+            placeholder="/path/to/mcap/files"
+            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+          />
+        </div>
+
+        {/* Display Name */}
+        <div>
+          <label
+            htmlFor="display_name"
+            className="block text-sm font-medium text-gray-700 mb-1"
+          >
+            Display Name
+          </label>
+          <input
+            id="display_name"
+            type="text"
+            value={formValues.display_name ?? ""}
+            onChange={(e) => handleChange("display_name", e.target.value)}
+            placeholder="SURF-WEC MODAQ Uploader"
+            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+          />
+        </div>
+
+        {/* Log Directory */}
+        <div>
+          <label
+            htmlFor="log_directory"
+            className="block text-sm font-medium text-gray-700 mb-1"
+          >
+            Log Directory
+          </label>
+          <input
+            id="log_directory"
+            type="text"
+            value={formValues.log_directory ?? ""}
+            onChange={(e) => handleChange("log_directory", e.target.value)}
+            placeholder="logs"
+            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+          />
+        </div>
+      </div>
+
+      {/* Connection test result */}
+      {testResult && (
+        <div
+          className={`mt-4 p-3 rounded-md text-sm ${
+            testResult.success
+              ? "bg-green-50 text-green-800 border border-green-200"
+              : "bg-red-50 text-red-800 border border-red-200"
+          }`}
+        >
+          {testResult.success ? testResult.message : testResult.error}
+        </div>
+      )}
+
+      {/* Buttons */}
+      <div className="mt-6 flex items-center gap-3">
+        <button
+          type="button"
+          onClick={handleTestConnection}
+          disabled={testing || !formValues.s3_bucket}
+          className="px-4 py-2 text-sm font-medium text-nlr-blue border border-nlr-blue rounded-md hover:bg-nlr-blue hover:text-white disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+        >
+          {testing ? "Testing..." : "Test Connection"}
+        </button>
+
+        <button
+          type="button"
+          onClick={handleSave}
+          disabled={saving || !isDirty}
+          className="px-4 py-2 text-sm font-medium text-white bg-nlr-blue rounded-md hover:bg-nlr-blue-light disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+        >
+          {saving ? "Saving..." : "Save Settings"}
+        </button>
+
+        {isDirty && (
+          <span className="text-sm text-nlr-yellow font-medium">
+            Unsaved changes
+          </span>
+        )}
+      </div>
+    </div>
+  );
+}
diff --git a/frontend/src/components/settings/UpdateSection.tsx b/frontend/src/components/settings/UpdateSection.tsx
new file mode 100644
index 0000000..ac7d3a6
--- /dev/null
+++ b/frontend/src/components/settings/UpdateSection.tsx
@@ -0,0 +1,143 @@
+import { useEffect, useState } from "react";
+import { apiGet, apiPost } from "../../api/client.ts";
+import { useAppStore } from "../../stores/appStore.ts";
+import type { UpdateCheckResult, UpdateResult } from "../../types/api.ts";
+
+export default function UpdateSection() {
+  const { version, loadVersion, addNotification } = useAppStore();
+
+  const [checkResult, setCheckResult] = useState<UpdateCheckResult | null>(null);
+  const [checking, setChecking] = useState(false);
+  const [updating, setUpdating] = useState(false);
+  const [updateResult, setUpdateResult] = useState<UpdateResult | null>(null);
+
+  useEffect(() => {
+    loadVersion();
+  }, [loadVersion]);
+
+  async function handleCheckUpdates() {
+    setChecking(true);
+    setCheckResult(null);
+    try {
+      const result = await apiGet<UpdateCheckResult>("/api/settings/check-updates");
+      setCheckResult(result);
+    } catch {
+      addNotification("error", "Failed to check for updates");
+    } finally {
+      setChecking(false);
+    }
+  }
+
+  async function handleUpdate() {
+    setUpdating(true);
+    setUpdateResult(null);
+    try {
+      const result = await apiPost<UpdateResult>("/api/settings/update");
+      setUpdateResult(result);
+      if (result.success) {
+        addNotification("success", "Application updated successfully");
+        loadVersion();
+      } else {
+        addNotification("warning", "Update completed with some errors");
+      }
+    } catch {
+      addNotification("error", "Failed to update application");
+    } finally {
+      setUpdating(false);
+    }
+  }
+
+  return (
+    <div className="bg-white rounded-lg shadow p-6">
+      <h3 className="text-lg font-semibold text-nlr-text mb-4">Application Updates</h3>
+
+      {/* Version info grid */}
+      {version && (
+        <div className="grid grid-cols-3 gap-4 mb-4">
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Version</div>
+            <div className="text-sm font-mono font-medium text-nlr-text mt-1">
+              {version.version}
+            </div>
+          </div>
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Commit</div>
+            <div className="text-sm font-mono font-medium text-nlr-text mt-1">
+              {version.commit.slice(0, 7)}
+              {version.dirty && <span className="text-nlr-yellow ml-1">(dirty)</span>}
+            </div>
+          </div>
+          <div className="bg-gray-50 rounded-md p-3">
+            <div className="text-xs text-gray-500 uppercase tracking-wide">Branch</div>
+            <div className="text-sm font-mono font-medium text-nlr-text mt-1">
+              {version.branch}
+            </div>
+          </div>
+        </div>
+      )}
+
+      {/* Update check result */}
+      {checkResult && (
+        <div
+          className={`mb-4 p-3 rounded-md text-sm ${
+            checkResult.updates_available
+              ? "bg-nlr-yellow/10 text-nlr-text border border-nlr-yellow/30"
+              : "bg-green-50 text-green-800 border border-green-200"
+          }`}
+        >
+          {checkResult.updates_available
+            ? `${checkResult.commits_behind} commit${checkResult.commits_behind !== 1 ? "s" : ""} behind remote`
+            : "Up to date"}
+        </div>
+      )}
+
+      {/* Update result log */}
+      {updateResult && (
+        <div className="mb-4 bg-gray-900 text-gray-100 rounded-md p-4 text-sm font-mono overflow-auto max-h-64">
+          {Object.entries(updateResult.results).map(([step, result]) => (
+            <div key={step} className="mb-3 last:mb-0">
+              <div className="flex items-center gap-2 mb-1">
+                <span
+                  className={`inline-block px-2 py-0.5 rounded text-xs font-semibold ${
+                    result.success
+                      ? "bg-green-600 text-white"
+                      : "bg-red-600 text-white"
+                  }`}
+                >
+                  {result.success ? "OK" : "FAIL"}
+                </span>
+                <span className="text-gray-300">{step}</span>
+              </div>
+              <pre className="text-xs text-gray-400 whitespace-pre-wrap pl-4">
+                {result.output || "(no output)"}
+              </pre>
+            </div>
+          ))}
+        </div>
+      )}
+
+      {/* Buttons */}
+      <div className="flex items-center gap-3">
+        <button
+          type="button"
+          onClick={handleCheckUpdates}
+          disabled={checking}
+          className="px-4 py-2 text-sm font-medium text-nlr-blue border border-nlr-blue rounded-md hover:bg-nlr-blue hover:text-white disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+        >
+          {checking ? "Checking..." : "Check for Updates"}
+        </button>
+
+        {checkResult?.updates_available && (
+          <button
+            type="button"
+            onClick={handleUpdate}
+            disabled={updating}
+            className="px-4 py-2 text-sm font-medium text-white bg-nlr-green rounded-md hover:bg-nlr-green-light disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+          >
+            {updating ? "Updating..." : "Update Application"}
+          </button>
+        )}
+      </div>
+    </div>
+  );
+}

From db2e85b14f9ba7e9e1fd6016d09269e69e3ff893 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:51:40 -0700
Subject: [PATCH 089/173] Frontend: Add upload page leveraging components

---
 frontend/src/pages/UploadPage.tsx | 396 ++++++++++++++++++++++++++++++
 1 file changed, 396 insertions(+)
 create mode 100644 frontend/src/pages/UploadPage.tsx

diff --git a/frontend/src/pages/UploadPage.tsx b/frontend/src/pages/UploadPage.tsx
new file mode 100644
index 0000000..146c136
--- /dev/null
+++ b/frontend/src/pages/UploadPage.tsx
@@ -0,0 +1,396 @@
+/**
+ * Upload page — the 4-step upload workflow with a unified file table.
+ *
+ * Step 1: FolderBrowser — select a folder of MCAP files
+ * Steps 2-4: Unified table that persists across Review, Upload, and Summary,
+ *   with phase-aware header, toolbar, and footer.
+ */
+
+import { useCallback, useEffect, useLayoutEffect, useMemo, useState } from "react";
+
+import ConfirmModal from "../components/upload/ConfirmModal.tsx";
+import FolderBrowser from "../components/upload/FolderBrowser.tsx";
+import type { FolderExclusions } from "../components/upload/FolderBrowser.tsx";
+import ReviewToolbar, { StatusFilterBar } from "../components/upload/ReviewToolbar.tsx";
+import Stepper from "../components/upload/Stepper.tsx";
+import UnifiedFileTable from "../components/upload/UnifiedFileTable.tsx";
+import UploadFooter from "../components/upload/UploadFooter.tsx";
+import UploadHeader from "../components/upload/UploadHeader.tsx";
+import { useFileStore } from "../hooks/useFileStore.ts";
+import { useFolderScan } from "../hooks/useFolderScan.ts";
+import { useUploadJob } from "../hooks/useUploadJob.ts";
+import { useAppStore } from "../stores/appStore.ts";
+import { useUploadStore, type UploadStep } from "../stores/uploadStore.ts";
+import type { FileUploadState, ScannedFileInfo } from "../types/api.ts";
+import type { StatusFilter, UploadPhase } from "../types/upload.ts";
+import { downloadUploadCsv } from "../utils/csv.ts";
+
+export default function UploadPage() {
+  const {
+    step,
+    setStep,
+    folderPath,
+    setFolderPath,
+    scanFolders,
+    scanTotals,
+    completedJob,
+    reset,
+  } = useUploadStore();
+
+  const defaultUploadFolder = useAppStore((s) => s.settings?.default_upload_folder);
+
+  const {
+    startScan,
+    cancelScan,
+    isScanning,
+    scanComplete,
+    folders,
+    totals,
+  } = useFolderScan();
+
+  const uploadJob = useUploadJob();
+
+  // Unified file store
+  const { files, store } = useFileStore();
+
+  // Local state
+  const [showConfirmModal, setShowConfirmModal] = useState(false);
+  const [pendingSelectedPaths, setPendingSelectedPaths] = useState<string[]>([]);
+  const [selectedPaths, setSelectedPaths] = useState<Set<string>>(new Set());
+
+  // Derive phase from step
+  const phase: UploadPhase = step <= 2 ? "review" : step === 3 ? "uploading" : "summary";
+
+  // ── Wire SSE callbacks to FileStore (useLayoutEffect to avoid race) ──
+
+  useLayoutEffect(() => {
+    uploadJob.onFileUpdate.current = (file: FileUploadState) => {
+      const statusMap: Record<string, "in_progress" | "completed" | "skipped" | "failed" | "queued"> = {
+        analyzing: "in_progress",
+        uploading: "in_progress",
+        completed: "completed",
+        skipped: "skipped",
+        failed: "failed",
+        cancelled: "failed",
+      };
+      store.updateFile(file.local_path, {
+        status: statusMap[file.status] ?? "queued",
+        progressPercent: file.progress_percent,
+        s3Path: file.s3_path || undefined,
+        error: file.error_message || undefined,
+        duration: file.upload_duration_seconds,
+        speed: file.upload_speed_mbps,
+      });
+    };
+    uploadJob.onCompletion.current = (completionFiles: FileUploadState[]) => {
+      store.mergeCompletion(completionFiles);
+    };
+  });
+
+  // ── Sync FileStore from scan data as folders arrive ──
+
+  useEffect(() => {
+    if (folders.length > 0 && step >= 2) {
+      store.buildFromScan(folders);
+      // Auto-select new files
+      const newSelected = new Set<string>();
+      for (const folder of folders) {
+        for (const file of folder.files) {
+          if (!file.already_uploaded) {
+            newSelected.add(file.path);
+          }
+        }
+      }
+      setSelectedPaths(newSelected);
+    }
+  }, [folders, step, store]);
+
+  // ── Freeze/unfreeze sort on phase transitions ──
+
+  useEffect(() => {
+    if (step === 3) store.freezeSort();
+    if (step === 4) store.unfreezeSort();
+  }, [step, store]);
+
+  // ── Step transitions ──
+
+  /** Step 1 -> 2: User selected a folder. Start scanning and advance. */
+  const handleFolderSelected = useCallback(
+    async (path: string, exclusions?: FolderExclusions) => {
+      store.clear();
+      setFolderPath(path);
+      setStep(2);
+      await startScan(path, false, exclusions);
+    },
+    [setFolderPath, setStep, startScan, store],
+  );
+
+  /** Step 2: User clicks "Start Upload" — show confirmation modal. */
+  const handleStartUploadClick = useCallback(() => {
+    setPendingSelectedPaths(Array.from(selectedPaths));
+    setShowConfirmModal(true);
+  }, [selectedPaths]);
+
+  /** Confirm modal: Start the actual upload, advance to step 3. */
+  const handleConfirmUpload = useCallback(
+    async (skipDuplicates: boolean) => {
+      setShowConfirmModal(false);
+      if (pendingSelectedPaths.length === 0) return;
+
+      // Mark selected files as queued, remove unselected
+      store.markSelectedAsPending(new Set(pendingSelectedPaths));
+      // Reset filter for upload phase
+      store.setFilter("all");
+      store.setSearch("");
+
+      setStep(3);
+      await uploadJob.startUpload(pendingSelectedPaths, skipDuplicates);
+    },
+    [pendingSelectedPaths, setStep, uploadJob, store],
+  );
+
+  /** Step 3 -> 4: Upload finished, advance to completion. */
+  useEffect(() => {
+    if (step === 3 && !uploadJob.isRunning && completedJob) {
+      setStep(4);
+    }
+  }, [step, uploadJob.isRunning, completedJob, setStep]);
+
+  /** Step 4 -> 1: Reset and start over. */
+  const handleUploadMore = useCallback(() => {
+    store.clear();
+    reset();
+  }, [reset, store]);
+
+  /** Back from step 2 -> step 1. */
+  const handleBack = useCallback(async () => {
+    if (isScanning) {
+      await cancelScan();
+    }
+    store.clear();
+    reset();
+  }, [isScanning, cancelScan, reset, store]);
+
+  /** Stepper click — only steps 1 and 2 are clickable, and only when not uploading. */
+  const handleStepClick = useCallback(
+    (s: UploadStep) => {
+      if (s === 1) {
+        handleBack();
+      } else if (s === 2 && step > 2) {
+        setStep(2);
+      }
+    },
+    [handleBack, step, setStep],
+  );
+
+  // ── Selection helpers ──
+
+  const toggleFile = useCallback((path: string) => {
+    setSelectedPaths((prev) => {
+      const next = new Set(prev);
+      if (next.has(path)) next.delete(path);
+      else next.add(path);
+      return next;
+    });
+  }, []);
+
+  const allFiles = useMemo(() => Array.from(store.getAllRows().values()), [files]);
+
+  const toggleAllFiltered = useCallback(() => {
+    const filteredPaths = files.map((f) => f.path);
+    const allSelected = filteredPaths.every((p) => selectedPaths.has(p));
+    setSelectedPaths((prev) => {
+      const next = new Set(prev);
+      for (const p of filteredPaths) {
+        if (allSelected) next.delete(p);
+        else next.add(p);
+      }
+      return next;
+    });
+  }, [files, selectedPaths]);
+
+  const selectAll = useCallback(() => {
+    setSelectedPaths(new Set(allFiles.map((f) => f.path)));
+  }, [allFiles]);
+
+  const selectNewOnly = useCallback(() => {
+    setSelectedPaths(new Set(allFiles.filter((f) => !f.alreadyUploaded).map((f) => f.path)));
+  }, [allFiles]);
+
+  const deselectAll = useCallback(() => {
+    setSelectedPaths(new Set());
+  }, []);
+
+  const selectFirstN = useCallback((n: number) => {
+    const paths = files.slice(0, n).map((f) => f.path);
+    setSelectedPaths(new Set(paths));
+  }, [files]);
+
+  // ── Header checkbox state ──
+
+  const filteredSelectedCount = files.filter((f) => selectedPaths.has(f.path)).length;
+  const headerChecked = files.length > 0 && filteredSelectedCount === files.length;
+  const headerIndeterminate = filteredSelectedCount > 0 && filteredSelectedCount < files.length;
+
+  // ── Selected new count (for start upload button) ──
+
+  const selectedNewCount = allFiles.filter(
+    (f) => selectedPaths.has(f.path) && !f.alreadyUploaded,
+  ).length;
+
+  // ── Confirm modal totals ──
+
+  const selectedTotals = useMemo(() => {
+    const selectedSet = new Set(pendingSelectedPaths);
+    let totalFiles = 0;
+    let alreadyUploaded = 0;
+    let totalSize = 0;
+    for (const folder of scanFolders) {
+      for (const file of folder.files as ScannedFileInfo[]) {
+        if (selectedSet.has(file.path)) {
+          totalFiles++;
+          totalSize += file.size;
+          if (file.already_uploaded) alreadyUploaded++;
+        }
+      }
+    }
+    return { totalFiles, alreadyUploaded, totalSize };
+  }, [pendingSelectedPaths, scanFolders]);
+
+  // ── Filter click handler (from clickable status counters) ──
+
+  const handleFilterClick = useCallback((filter: StatusFilter) => {
+    store.setFilter(filter);
+  }, [store]);
+
+  // ── CSV download ──
+
+  const handleDownloadCsv = useCallback(() => {
+    const jobId = completedJob?.job_id ?? "unknown";
+    downloadUploadCsv(Array.from(store.getAllRows().values()), jobId);
+  }, [completedJob, store]);
+
+  // ── Active totals for header ──
+
+  const activeTotals = scanComplete ? totals : scanTotals;
+
+  // ── Render ──
+
+  return (
+    <div>
+      <Stepper
+        currentStep={step}
+        onStepClick={handleStepClick}
+        isUploading={step === 3 && uploadJob.isRunning}
+      />
+
+      {step === 1 && (
+        <FolderBrowser
+          onFolderSelected={handleFolderSelected}
+          initialPath={folderPath || defaultUploadFolder || undefined}
+        />
+      )}
+
+      {step >= 2 && (
+        <div className="space-y-4">
+          {/* Phase-aware header (stat cards / progress / summary) */}
+          <UploadHeader
+            phase={phase}
+            totals={activeTotals}
+            isScanning={isScanning}
+            foldersFound={folders.length}
+            progressPercent={uploadJob.progressPercent}
+            filesProcessed={uploadJob.filesProcessed}
+            totalFiles={uploadJob.totalFiles}
+            statusCounts={uploadJob.statusCounts}
+            eta={uploadJob.eta}
+            isRunning={uploadJob.isRunning}
+            uploadedBytesFormatted={uploadJob.uploadedBytesFormatted}
+            totalBytesFormatted={uploadJob.totalBytesFormatted}
+            job={completedJob}
+            onFilterClick={handleFilterClick}
+          />
+
+          {/* Phase-aware toolbar */}
+          {phase === "review" ? (
+            <ReviewToolbar
+              statusFilter={store.getFilter()}
+              onStatusFilterChange={(f) => store.setFilter(f)}
+              searchQuery={store.getSearch()}
+              onSearchChange={(q) => store.setSearch(q)}
+              selectedCount={selectedPaths.size}
+              totalCount={store.getSize()}
+              filteredCount={files.length}
+              showFilteredCount={store.getFilter() !== "all" || store.getSearch() !== ""}
+              onSelectAll={selectAll}
+              onSelectNewOnly={selectNewOnly}
+              onToggleAllFiltered={toggleAllFiltered}
+              onDeselectAll={deselectAll}
+              onSelectFirstN={selectFirstN}
+              headerChecked={headerChecked}
+            />
+          ) : (
+            <StatusFilterBar
+              filter={store.getFilter()}
+              onFilterChange={(f) => store.setFilter(f)}
+              totalCount={store.getSize()}
+              filteredCount={files.length}
+              searchQuery={store.getSearch()}
+              onSearchChange={(q) => store.setSearch(q)}
+            />
+          )}
+
+          {/* Top action buttons (review phase only) */}
+          {phase === "review" && (
+            <UploadFooter
+              phase="review"
+              onBack={handleBack}
+              onStartUpload={handleStartUploadClick}
+              selectedNewCount={selectedNewCount}
+            />
+          )}
+
+          {/* The unified file table — stays mounted across phases */}
+          <UnifiedFileTable
+            phase={phase}
+            files={files}
+            sortKey={store.getSortKey()}
+            sortDir={store.getSortDir()}
+            onSort={(key) => store.setSort(key)}
+            isSortFrozen={store.isFrozen()}
+            selectedPaths={selectedPaths}
+            onToggleFile={toggleFile}
+            onToggleAllFiltered={toggleAllFiltered}
+            headerChecked={headerChecked}
+            headerIndeterminate={headerIndeterminate}
+          />
+
+          {/* Bottom action buttons */}
+          <UploadFooter
+            phase={phase}
+            onBack={handleBack}
+            onStartUpload={handleStartUploadClick}
+            selectedNewCount={selectedNewCount}
+            onCancel={uploadJob.cancelUpload}
+            isRunning={uploadJob.isRunning}
+            onDownloadCsv={handleDownloadCsv}
+            onUploadMore={handleUploadMore}
+            failedCount={uploadJob.statusCounts.failed}
+          />
+
+          {/* Confirm modal */}
+          {step === 2 && (
+            <ConfirmModal
+              isOpen={showConfirmModal}
+              onClose={() => setShowConfirmModal(false)}
+              onConfirm={handleConfirmUpload}
+              totalFiles={selectedTotals.totalFiles}
+              alreadyUploaded={selectedTotals.alreadyUploaded}
+              totalSize={selectedTotals.totalSize}
+            />
+          )}
+        </div>
+      )}
+    </div>
+  );
+}

From a04ef95f13df47964b96f9579caf2fe25d8e14fb Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:52:09 -0700
Subject: [PATCH 090/173] Frontend: Add Settings page leveraging components

---
 frontend/src/pages/SettingsPage.tsx | 32 +++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 frontend/src/pages/SettingsPage.tsx

diff --git a/frontend/src/pages/SettingsPage.tsx b/frontend/src/pages/SettingsPage.tsx
new file mode 100644
index 0000000..cf2a901
--- /dev/null
+++ b/frontend/src/pages/SettingsPage.tsx
@@ -0,0 +1,32 @@
+import { useEffect } from "react";
+import CacheSection from "../components/settings/CacheSection.tsx";
+import DangerZone from "../components/settings/DangerZone.tsx";
+import SettingsForm from "../components/settings/SettingsForm.tsx";
+import UpdateSection from "../components/settings/UpdateSection.tsx";
+import { useAppStore } from "../stores/appStore.ts";
+
+export default function SettingsPage() {
+  const { loadSettings, settingsLoading } = useAppStore();
+
+  useEffect(() => {
+    loadSettings();
+  }, [loadSettings]);
+
+  if (settingsLoading) {
+    return (
+      <div className="flex items-center justify-center py-12">
+        <div className="spinner h-8 w-8 border-4 border-nlr-blue border-t-transparent rounded-full" />
+      </div>
+    );
+  }
+
+  return (
+    <div className="max-w-3xl mx-auto space-y-6">
+      <h2 className="text-xl font-semibold text-nlr-text">Settings</h2>
+      <SettingsForm />
+      <UpdateSection />
+      <CacheSection />
+      <DangerZone />
+    </div>
+  );
+}

From fcf6c0ee4070df42e4c69467cfcbffbe47d81049 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:52:49 -0700
Subject: [PATCH 091/173] Frontend: Add S3 file browser page

---
 frontend/src/pages/FilesPage.tsx | 38 ++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 frontend/src/pages/FilesPage.tsx

diff --git a/frontend/src/pages/FilesPage.tsx b/frontend/src/pages/FilesPage.tsx
new file mode 100644
index 0000000..1c4e83f
--- /dev/null
+++ b/frontend/src/pages/FilesPage.tsx
@@ -0,0 +1,38 @@
+import { useEffect } from "react";
+import S3Browser from "../components/files/S3Browser.tsx";
+import { useAppStore } from "../stores/appStore.ts";
+
+export default function FilesPage() {
+  const settings = useAppStore((s) => s.settings);
+  const loadSettings = useAppStore((s) => s.loadSettings);
+
+  useEffect(() => {
+    if (!settings) {
+      void loadSettings();
+    }
+  }, [settings, loadSettings]);
+
+  if (!settings) {
+    return (
+      <div className="text-center py-12 text-gray-500">Loading settings...</div>
+    );
+  }
+
+  if (!settings.s3_bucket) {
+    return (
+      <div className="text-center py-12">
+        <p className="text-gray-500 mb-2">S3 bucket is not configured.</p>
+        <a href="/settings" className="text-sm text-nlr-blue hover:underline">
+          Go to Settings
+        </a>
+      </div>
+    );
+  }
+
+  return (
+    <div>
+      <h2 className="text-xl font-semibold text-nlr-text mb-4">Browse Uploaded Files</h2>
+      <S3Browser bucketName={settings.s3_bucket} region={settings.aws_region} />
+    </div>
+  );
+}

From 1e14d47afc6ad4bef5107122ee52139625ed2891 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:59:20 -0700
Subject: [PATCH 092/173] Frontend: Add delete page

---
 frontend/src/pages/DeletePage.tsx | 414 ++++++++++++++++++++++++++++++
 1 file changed, 414 insertions(+)
 create mode 100644 frontend/src/pages/DeletePage.tsx

diff --git a/frontend/src/pages/DeletePage.tsx b/frontend/src/pages/DeletePage.tsx
new file mode 100644
index 0000000..56017e5
--- /dev/null
+++ b/frontend/src/pages/DeletePage.tsx
@@ -0,0 +1,414 @@
+/**
+ * Delete page — 5-step workflow for deleting local files after S3 upload.
+ *
+ * Step 1: FolderBrowser — select a folder
+ * Step 2: Review matched files with stats
+ * Step 3: Confirmation (type DELETE + checkbox)
+ * Step 4: Progress (verification + deletion with SSE)
+ * Step 5: Summary with results
+ */
+
+import { useCallback, useEffect, useMemo, useState } from "react";
+
+import ProgressBar from "../components/common/ProgressBar.tsx";
+import StatCard from "../components/common/StatCard.tsx";
+import DeleteConfirmation from "../components/delete/DeleteConfirmation.tsx";
+import DeleteStepper from "../components/delete/DeleteStepper.tsx";
+import FolderBrowser from "../components/upload/FolderBrowser.tsx";
+import { useDeleteJob } from "../hooks/useDeleteJob.ts";
+import { useDeleteScan } from "../hooks/useDeleteScan.ts";
+import { useAppStore } from "../stores/appStore.ts";
+import { useDeleteStore, type DeleteStep } from "../stores/deleteStore.ts";
+import type { DeleteScanFile } from "../types/delete.ts";
+import { formatBytes } from "../utils/format/bytes.ts";
+
+/** Status badge colors for file table. */
+function statusBadge(status: string) {
+  switch (status) {
+    case "deleted":
+      return "bg-green-100 text-green-700";
+    case "verified":
+      return "bg-blue-100 text-blue-700";
+    case "verifying":
+    case "deleting":
+      return "bg-yellow-100 text-yellow-700";
+    case "mismatch":
+      return "bg-orange-100 text-orange-700";
+    case "failed":
+      return "bg-red-100 text-red-700";
+    case "cancelled":
+      return "bg-gray-100 text-gray-600";
+    default:
+      return "bg-gray-100 text-gray-600";
+  }
+}
+
+/** Truncate path for display, showing last N segments. */
+function truncatePath(path: string, segments = 3): string {
+  const parts = path.split("/");
+  if (parts.length <= segments) return path;
+  return `.../${parts.slice(-segments).join("/")}`;
+}
+
+export default function DeletePage() {
+  const {
+    step,
+    setStep,
+    folderPath,
+    setFolderPath,
+    scanResults,
+    scanTotalSize,
+    completedJob,
+    isDeleting,
+    reset,
+  } = useDeleteStore();
+
+  const defaultUploadFolder = useAppStore(
+    (s) => s.settings?.default_upload_folder,
+  );
+
+  const { scan, isScanning } = useDeleteScan();
+  const deleteJob = useDeleteJob();
+
+  // Pagination for file table
+  const [page, setPage] = useState(0);
+  const pageSize = 50;
+
+  // ── Step transitions ──
+
+  const handleFolderSelected = useCallback(
+    async (path: string) => {
+      setFolderPath(path);
+      setStep(2);
+      await scan(path);
+    },
+    [setFolderPath, setStep, scan],
+  );
+
+  const handleConfirmDelete = useCallback(async () => {
+    setStep(4);
+    await deleteJob.startDelete();
+  }, [setStep, deleteJob]);
+
+  // Auto-advance from Step 4 to Step 5 when deletion completes
+  useEffect(() => {
+    if (step === 4 && !deleteJob.isRunning && completedJob) {
+      setStep(5);
+    }
+  }, [step, deleteJob.isRunning, completedJob, setStep]);
+
+  const handleStartOver = useCallback(() => {
+    reset();
+  }, [reset]);
+
+  const handleBack = useCallback(() => {
+    if (step === 2) {
+      reset();
+    } else if (step === 3) {
+      setStep(2);
+    }
+  }, [step, reset, setStep]);
+
+  const handleStepClick = useCallback(
+    (s: DeleteStep) => {
+      if (s === 1) reset();
+      else if (s === 2 && step > 2) setStep(2);
+    },
+    [reset, step, setStep],
+  );
+
+  // ── Derived data ──
+
+  const progressPercent = useMemo(() => {
+    if (deleteJob.totalFiles === 0) return 0;
+    return Math.round(
+      (deleteJob.filesProcessed / deleteJob.totalFiles) * 100,
+    );
+  }, [deleteJob.filesProcessed, deleteJob.totalFiles]);
+
+  const completionFiles: DeleteScanFile[] = completedJob?.files ?? [];
+
+  // Paginated files for review step
+  const paginatedReviewFiles = useMemo(() => {
+    const start = page * pageSize;
+    return scanResults.slice(start, start + pageSize);
+  }, [scanResults, page]);
+
+  const totalPages = Math.ceil(scanResults.length / pageSize);
+
+  // ── Render ──
+
+  return (
+    <div>
+      <DeleteStepper
+        currentStep={step}
+        onStepClick={handleStepClick}
+        isDeleting={isDeleting}
+      />
+
+      {/* Step 1: Folder Selection */}
+      {step === 1 && (
+        <FolderBrowser
+          onFolderSelected={handleFolderSelected}
+          initialPath={folderPath || defaultUploadFolder || undefined}
+          mode="delete"
+        />
+      )}
+
+      {/* Step 2: Review */}
+      {step === 2 && (
+        <div className="space-y-4">
+          <div className="grid grid-cols-3 gap-4">
+            <StatCard
+              value={scanResults.length}
+              label="Files Matched"
+              color="text-nlr-blue"
+            />
+            <StatCard
+              value={formatBytes(scanTotalSize)}
+              label="Total Size"
+              color="text-nlr-blue"
+            />
+            <StatCard
+              value={isScanning ? "Scanning..." : "Ready"}
+              label="Status"
+              color={isScanning ? "text-amber-600" : "text-green-600"}
+            />
+          </div>
+
+          {scanResults.length === 0 && !isScanning && (
+            <div className="bg-amber-50 border border-amber-200 rounded-lg p-4 text-sm text-amber-800">
+              No uploaded MCAP files found in this folder. Only files previously
+              uploaded through this application can be cleared.
+            </div>
+          )}
+
+          {scanResults.length > 0 && (
+            <>
+              <div className="bg-white rounded-lg border border-gray-200 overflow-hidden">
+                <table className="w-full text-sm">
+                  <thead className="bg-gray-50 border-b border-gray-200">
+                    <tr>
+                      <th className="text-left px-4 py-2 font-medium text-gray-600">
+                        Filename
+                      </th>
+                      <th className="text-left px-4 py-2 font-medium text-gray-600">
+                        Size
+                      </th>
+                      <th className="text-left px-4 py-2 font-medium text-gray-600">
+                        S3 Path
+                      </th>
+                    </tr>
+                  </thead>
+                  <tbody className="divide-y divide-gray-100">
+                    {paginatedReviewFiles.map((f) => (
+                      <tr key={f.local_path} className="hover:bg-gray-50">
+                        <td className="px-4 py-2 font-mono text-xs">
+                          {f.filename}
+                        </td>
+                        <td className="px-4 py-2 text-gray-600">
+                          {formatBytes(f.file_size)}
+                        </td>
+                        <td
+                          className="px-4 py-2 text-gray-500 text-xs"
+                          title={f.s3_path}
+                        >
+                          {truncatePath(f.s3_path)}
+                        </td>
+                      </tr>
+                    ))}
+                  </tbody>
+                </table>
+              </div>
+
+              {/* Pagination */}
+              {totalPages > 1 && (
+                <div className="flex items-center justify-between text-sm text-gray-600">
+                  <span>
+                    Showing {page * pageSize + 1}–
+                    {Math.min((page + 1) * pageSize, scanResults.length)} of{" "}
+                    {scanResults.length}
+                  </span>
+                  <div className="flex gap-2">
+                    <button
+                      type="button"
+                      onClick={() => setPage((p) => Math.max(0, p - 1))}
+                      disabled={page === 0}
+                      className="px-3 py-1 border rounded disabled:opacity-50"
+                    >
+                      Prev
+                    </button>
+                    <button
+                      type="button"
+                      onClick={() =>
+                        setPage((p) => Math.min(totalPages - 1, p + 1))
+                      }
+                      disabled={page >= totalPages - 1}
+                      className="px-3 py-1 border rounded disabled:opacity-50"
+                    >
+                      Next
+                    </button>
+                  </div>
+                </div>
+              )}
+            </>
+          )}
+
+          <div className="flex gap-3">
+            <button
+              type="button"
+              onClick={handleBack}
+              className="px-4 py-2 text-sm font-medium text-gray-700 bg-white border border-gray-300 rounded-md hover:bg-gray-50"
+            >
+              Back
+            </button>
+            {scanResults.length > 0 && (
+              <button
+                type="button"
+                onClick={() => setStep(3)}
+                disabled={isScanning}
+                className="px-4 py-2 text-sm font-medium text-white bg-red-600 rounded-md hover:bg-red-700 disabled:bg-gray-300 disabled:cursor-not-allowed"
+              >
+                Continue to Confirmation
+              </button>
+            )}
+          </div>
+        </div>
+      )}
+
+      {/* Step 3: Confirmation */}
+      {step === 3 && (
+        <DeleteConfirmation
+          totalFiles={scanResults.length}
+          totalSize={scanTotalSize}
+          onConfirm={handleConfirmDelete}
+          onBack={handleBack}
+        />
+      )}
+
+      {/* Step 4: Deletion Progress */}
+      {step === 4 && (
+        <div className="space-y-4">
+          <div className="grid grid-cols-3 gap-4">
+            <StatCard
+              value={deleteJob.statusCounts.verified + deleteJob.statusCounts.deleted}
+              label="Verified"
+              color="text-blue-600"
+            />
+            <StatCard
+              value={deleteJob.statusCounts.deleted}
+              label="Cleared"
+              color="text-green-600"
+            />
+            <StatCard
+              value={deleteJob.statusCounts.mismatch + deleteJob.statusCounts.failed}
+              label="Skipped"
+              color="text-amber-600"
+            />
+          </div>
+
+          <ProgressBar
+            percent={progressPercent}
+            label={
+              deleteJob.jobStatus === "verifying"
+                ? "Verifying files against S3..."
+                : deleteJob.jobStatus === "deleting"
+                  ? "Clearing verified files..."
+                  : "Processing..."
+            }
+          />
+
+          <button
+            type="button"
+            onClick={deleteJob.cancelDelete}
+            className="px-4 py-2 text-sm font-medium text-red-700 bg-red-50 border border-red-200 rounded-md hover:bg-red-100"
+          >
+            Cancel
+          </button>
+        </div>
+      )}
+
+      {/* Step 5: Summary */}
+      {step === 5 && completedJob && (
+        <div className="space-y-4">
+          <div className="grid grid-cols-2 sm:grid-cols-4 gap-4">
+            <StatCard
+              value={completedJob.status_counts.deleted ?? 0}
+              label="Cleared"
+              color="text-green-600"
+            />
+            <StatCard
+              value={completedJob.status_counts.mismatch ?? 0}
+              label="Mismatched"
+              color="text-amber-600"
+            />
+            <StatCard
+              value={completedJob.status_counts.failed ?? 0}
+              label="Failed"
+              color="text-red-600"
+            />
+            <StatCard
+              value={formatBytes(completedJob.total_deleted_size)}
+              label="Space Freed"
+              color="text-nlr-blue"
+            />
+          </div>
+
+          {/* Result file table */}
+          {completionFiles.length > 0 && (
+            <div className="bg-white rounded-lg border border-gray-200 overflow-hidden">
+              <table className="w-full text-sm">
+                <thead className="bg-gray-50 border-b border-gray-200">
+                  <tr>
+                    <th className="text-left px-4 py-2 font-medium text-gray-600">
+                      Filename
+                    </th>
+                    <th className="text-left px-4 py-2 font-medium text-gray-600">
+                      Size
+                    </th>
+                    <th className="text-left px-4 py-2 font-medium text-gray-600">
+                      Status
+                    </th>
+                    <th className="text-left px-4 py-2 font-medium text-gray-600">
+                      Details
+                    </th>
+                  </tr>
+                </thead>
+                <tbody className="divide-y divide-gray-100">
+                  {completionFiles.map((f) => (
+                    <tr key={f.local_path} className="hover:bg-gray-50">
+                      <td className="px-4 py-2 font-mono text-xs">
+                        {f.filename}
+                      </td>
+                      <td className="px-4 py-2 text-gray-600">
+                        {formatBytes(f.file_size)}
+                      </td>
+                      <td className="px-4 py-2">
+                        <span
+                          className={`inline-block px-2 py-0.5 rounded-full text-xs font-medium ${statusBadge(f.status)}`}
+                        >
+                          {f.status}
+                        </span>
+                      </td>
+                      <td className="px-4 py-2 text-xs text-gray-500">
+                        {f.error_message || (f.verification === "md5+size" ? "Verified: MD5 + size" : f.verification === "size" ? "Verified: size (multipart ETag)" : "—")}
+                      </td>
+                    </tr>
+                  ))}
+                </tbody>
+              </table>
+            </div>
+          )}
+
+          <button
+            type="button"
+            onClick={handleStartOver}
+            className="px-4 py-2 text-sm font-medium text-white bg-nlr-blue rounded-md hover:bg-nlr-blue-light"
+          >
+            Clear More Files
+          </button>
+        </div>
+      )}
+    </div>
+  );
+}

From b98026765caff9beccb5015e0fec9de0c08b632e Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 16:59:43 -0700
Subject: [PATCH 093/173] Frontend: Add Logs page

---
 frontend/src/pages/LogsPage.tsx | 78 +++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 frontend/src/pages/LogsPage.tsx

diff --git a/frontend/src/pages/LogsPage.tsx b/frontend/src/pages/LogsPage.tsx
new file mode 100644
index 0000000..8b0b997
--- /dev/null
+++ b/frontend/src/pages/LogsPage.tsx
@@ -0,0 +1,78 @@
+import { useCallback, useState } from "react";
+import FilterBar from "../components/logs/FilterBar.tsx";
+import type { LogFilters } from "../components/logs/FilterBar.tsx";
+import LogStatsBar from "../components/logs/LogStatsBar.tsx";
+import LogTable from "../components/logs/LogTable.tsx";
+import UploadSessionList from "../components/logs/UploadSessionList.tsx";
+import UploadStatsBar from "../components/logs/UploadStatsBar.tsx";
+import type { UploadSession, UploadStatsResponse } from "../types/api.ts";
+
+type ActiveTab = "uploads" | "events";
+
+const DEFAULT_FILTERS: LogFilters = {
+  date: "",
+  level: "",
+  category: "",
+  search: "",
+};
+
+const tabs: { key: ActiveTab; label: string }[] = [
+  { key: "uploads", label: "Upload History" },
+  { key: "events", label: "Event Log" },
+];
+
+export default function LogsPage() {
+  const [activeTab, setActiveTab] = useState<ActiveTab>("uploads");
+  const [filters, setFilters] = useState<LogFilters>(DEFAULT_FILTERS);
+  const [sessions, setSessions] = useState<UploadSession[]>([]);
+
+  const handleUploadDataLoaded = useCallback((data: UploadStatsResponse) => {
+    setSessions(data.sessions);
+  }, []);
+
+  const handleFilterChange = useCallback((newFilters: LogFilters) => {
+    setFilters(newFilters);
+  }, []);
+
+  const title = activeTab === "uploads" ? "Upload History" : "Event Log";
+
+  return (
+    <div>
+      <h2 className="text-xl font-semibold text-nlr-text mb-4">{title}</h2>
+
+      {/* Tab bar */}
+      <div className="flex border-b border-gray-200 mb-6">
+        {tabs.map((tab) => (
+          <button
+            key={tab.key}
+            onClick={() => setActiveTab(tab.key)}
+            className={`px-4 py-2 text-sm font-medium transition-colors -mb-px ${
+              activeTab === tab.key
+                ? "text-nlr-blue border-b-2 border-nlr-blue"
+                : "text-gray-500 hover:text-gray-700"
+            }`}
+          >
+            {tab.label}
+          </button>
+        ))}
+      </div>
+
+      {/* Upload History tab */}
+      {activeTab === "uploads" && (
+        <div className="space-y-6">
+          <UploadStatsBar onDataLoaded={handleUploadDataLoaded} />
+          <UploadSessionList sessions={sessions} />
+        </div>
+      )}
+
+      {/* Event Log tab */}
+      {activeTab === "events" && (
+        <div className="space-y-6">
+          <LogStatsBar />
+          <FilterBar onFilterChange={handleFilterChange} />
+          <LogTable filters={filters} />
+        </div>
+      )}
+    </div>
+  );
+}

From 1ccf1ece0b2255422a93743b0db58381f604ca40 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 17:02:31 -0700
Subject: [PATCH 094/173] Refactor: Remove deprecated jinja templates

---
 app/templates/base.html     | 399 ---------------------------------
 app/templates/files.html    | 106 ---------
 app/templates/index.html    | 430 ------------------------------------
 app/templates/logs.html     | 169 --------------
 app/templates/macros.html   |  16 --
 app/templates/settings.html | 241 --------------------
 6 files changed, 1361 deletions(-)
 delete mode 100644 app/templates/base.html
 delete mode 100644 app/templates/files.html
 delete mode 100644 app/templates/index.html
 delete mode 100644 app/templates/logs.html
 delete mode 100644 app/templates/macros.html
 delete mode 100644 app/templates/settings.html

diff --git a/app/templates/base.html b/app/templates/base.html
deleted file mode 100644
index bbdf0aa..0000000
--- a/app/templates/base.html
+++ /dev/null
@@ -1,399 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
-    <meta charset="UTF-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>{% block title %}{{ display_name }}{% endblock %}</title>
-
-    <!-- Google Fonts - Roboto (NLR standard) -->
-    <link href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700&display=swap" rel="stylesheet">
-
-    <!-- Tailwind CSS CDN -->
-    <script src="https://cdn.tailwindcss.com"></script>
-
-    <!-- Tailwind Configuration with NLR Brand Colors -->
-    <script>
-        tailwind.config = {
-            theme: {
-                extend: {
-                    fontFamily: {
-                        'roboto': ['Roboto', 'Helvetica Neue', 'Helvetica', 'sans-serif'],
-                    },
-                    colors: {
-                        'nlr': {
-                            'blue': '#0079C2',
-                            'blue-light': '#00A3E4',
-                            'yellow': '#EE9521',
-                            'yellow-light': '#FFC423',
-                            'green': '#5D9732',
-                            'green-light': '#9ECE42',
-                            'gray': '#5E6A71',
-                            'gray-light': '#D1D5D8',
-                            'gray-bg': '#EDEDED',
-                            'gray-footer': '#E3E6E8',
-                            'text': '#212224',
-                        }
-                    }
-                }
-            }
-        }
-    </script>
-
-    <!-- Custom Styles based on NLR Branding -->
-    <style>
-        body {
-            font-family: 'Roboto', 'Helvetica Neue', Helvetica, sans-serif;
-        }
-
-        /* Header styles matching NLR branding */
-        .nlr-header {
-            background: #fff;
-            width: 100%;
-        }
-
-        .nlr-header-top {
-            display: flex;
-            align-items: center;
-            justify-content: space-between;
-            height: 100px;
-            max-width: 1140px;
-            margin: 0 auto;
-            padding: 0 15px;
-        }
-
-        .nlr-header-title {
-            font-weight: normal;
-            color: #212224;
-            font-size: 24px;
-            letter-spacing: 0.5px;
-        }
-
-        .nlr-logo-image {
-            width: 200px;
-        }
-
-        /* Menu bar styles */
-        .nlr-menu-bar {
-            background: #EDEDED;
-            border-top: 1px solid #D6D4D4;
-            height: 50px;
-        }
-
-        .nlr-menu-container {
-            max-width: 1140px;
-            margin: 0 auto;
-            display: flex;
-            align-items: center;
-            height: 100%;
-            padding: 0 15px;
-        }
-
-        .nlr-menu-item {
-            color: #2F2F2F;
-            padding: 14px 20px;
-            font-size: 14px;
-            text-decoration: none;
-            transition: all 0.2s;
-        }
-
-        .nlr-menu-item:hover,
-        .nlr-menu-item.active {
-            background: #5E6A71;
-            color: #fff;
-        }
-
-        /* Footer styles matching NLR branding */
-        .nlr-footer {
-            background-color: #E3E6E8;
-            font-size: 14px;
-            font-weight: 400;
-            line-height: 1.2;
-        }
-
-        .nlr-footer-top {
-            background-color: #D1D5D8;
-            padding: 1.5em 0;
-        }
-
-        .nlr-footer-bottom {
-            padding: 1.5em 0 3em 0;
-        }
-
-        .nlr-footer a {
-            color: #000;
-            text-decoration: none;
-        }
-
-        .nlr-footer a:hover {
-            color: #C60;
-            text-decoration: underline;
-        }
-
-        .nlr-attr {
-            font-size: 12px;
-        }
-
-        /* Drag and drop styling */
-        .drop-zone {
-            transition: all 0.3s ease;
-        }
-        .drop-zone.drag-over {
-            border-color: #0079C2;
-            background-color: rgba(0, 121, 194, 0.1);
-        }
-
-        /* Progress bar animation */
-        .progress-bar {
-            transition: width 0.4s ease-out;
-        }
-
-        /* Phase label fade transition */
-        #upload-phase-label {
-            transition: opacity 0.15s ease;
-        }
-
-        /* File item hover effect */
-        .file-item:hover {
-            background-color: rgba(0, 121, 194, 0.05);
-        }
-
-        /* Spinner animation */
-        @keyframes spin {
-            to { transform: rotate(360deg); }
-        }
-        .spinner {
-            animation: spin 1s linear infinite;
-        }
-
-        /* Upload Steps Indicator */
-        .step-circle {
-            transition: all 0.3s ease;
-        }
-        .step-label {
-            transition: all 0.3s ease;
-        }
-        .step-connector {
-            transition: all 0.3s ease;
-        }
-
-        /* Completed step - clickable to go back */
-        [data-step].completed {
-            cursor: pointer;
-        }
-        [data-step].completed:hover .step-circle {
-            transform: scale(1.1);
-            box-shadow: 0 2px 4px rgba(0,0,0,0.1);
-        }
-        [data-step].completed .step-circle {
-            background-color: #5D9732;
-            border-color: #5D9732;
-            color: white;
-            transition: transform 0.2s, box-shadow 0.2s;
-        }
-        [data-step].completed .step-label {
-            color: #5D9732;
-        }
-        [data-step].completed + .step-connector {
-            background-color: #5D9732;
-        }
-
-        /* Active/Current step */
-        [data-step].active .step-circle {
-            background-color: #0079C2;
-            border-color: #0079C2;
-            color: white;
-        }
-        [data-step].active .step-label {
-            color: #0079C2;
-            font-weight: 600;
-        }
-
-        /* Future steps - not clickable */
-        [data-step]:not(.completed):not(.active) {
-            cursor: default;
-        }
-
-        /* Responsive adjustments */
-        @media (max-width: 991px) {
-            .nlr-header-top {
-                max-width: 720px;
-            }
-            .nlr-menu-container {
-                max-width: 720px;
-            }
-        }
-
-        @media (max-width: 767px) {
-            .nlr-header-top {
-                flex-direction: column;
-                height: auto;
-                padding: 15px;
-                text-align: center;
-            }
-            .nlr-header-title {
-                font-size: 20px;
-                margin-top: 10px;
-            }
-            .nlr-logo-image {
-                width: 180px;
-            }
-            .nlr-menu-item {
-                padding: 12px 15px;
-                font-size: 13px;
-            }
-        }
-    </style>
-
-    {% block head %}{% endblock %}
-</head>
-<body class="bg-gray-50 min-h-screen flex flex-col font-roboto" {% block body_attrs %}{% endblock %}>
-    <!-- NLR Header -->
-    <header class="nlr-header">
-        <!-- Top section with title and logo -->
-        <div class="nlr-header-top">
-            <h1 class="nlr-header-title">{{ display_name }}</h1>
-            <a href="https://www.nlr.gov" target="_blank" rel="noopener noreferrer">
-                <img src="{{ url_for('static', filename='images/nlr-logo@2x-01.png') }}"
-                     alt="National Laboratory of the Rockies"
-                     class="nlr-logo-image">
-            </a>
-        </div>
-
-        <!-- Navigation menu bar -->
-        <nav class="nlr-menu-bar">
-            <div class="nlr-menu-container">
-                <a href="{{ url_for('main.index') }}"
-                   class="nlr-menu-item {% if request.endpoint == 'main.index' %}active{% endif %}">
-                    Upload
-                </a>
-                <a href="{{ url_for('main.files') }}"
-                   class="nlr-menu-item {% if request.endpoint == 'main.files' %}active{% endif %}">
-                    Browse Uploaded Files
-                </a>
-                <a href="{{ url_for('main.logs') }}"
-                   class="nlr-menu-item {% if request.endpoint == 'main.logs' %}active{% endif %}">
-                    Logs
-                </a>
-                <!-- Spacer to push right-side items -->
-                <div class="flex-grow"></div>
-                <!-- Version badge (clickable to open About modal) -->
-                <a href="{{ url_for('main.settings') }}"
-                   class="nlr-menu-item {% if request.endpoint == 'main.settings' %}active{% endif %}">
-                    Settings
-                </a>
-            </div>
-        </nav>
-    </header>
-
-    <!-- Flash Messages -->
-    {% with messages = get_flashed_messages(with_categories=true) %}
-        {% if messages %}
-            <div class="max-w-5xl mx-auto px-4 mt-4">
-                {% for category, message in messages %}
-                    <div class="rounded-md p-4 mb-2
-                                {% if category == 'error' %}bg-red-100 text-red-800
-                                {% elif category == 'success' %}bg-green-100 text-green-800
-                                {% else %}bg-blue-100 text-blue-800{% endif %}">
-                        <p class="text-sm font-medium">{{ message }}</p>
-                    </div>
-                {% endfor %}
-            </div>
-        {% endif %}
-    {% endwith %}
-
-    <!-- Main Content -->
-    <main class="max-w-5xl w-full mx-auto px-4 py-8 flex-grow">
-        {% block content %}{% endblock %}
-    </main>
-
-    <!-- NLR Footer -->
-    <footer class="nlr-footer mt-auto">
-        <!-- Footer Top -->
-        <div class="nlr-footer-top">
-            <div class="max-w-5xl mx-auto px-4">
-                <div class="flex flex-col md:flex-row justify-between items-start md:items-center">
-                    <div>
-                        <a href="https://www.nlr.gov" class="font-bold">National Laboratory of the Rockies</a>
-                    </div>
-                    <div class="flex flex-wrap gap-4 mt-2 md:mt-0 text-sm">
-                        <a href="https://www.nlr.gov/about/">About</a>
-                        <a href="https://www.nlr.gov/research/">Research</a>
-                        <a href="https://www.nlr.gov/workingwithus/">Work with Us</a>
-                        <a href="https://www.nlr.gov/news/">News</a>
-                    </div>
-                </div>
-            </div>
-        </div>
-
-        <!-- Footer Bottom -->
-        <div class="nlr-footer-bottom">
-            <div class="max-w-5xl mx-auto px-4">
-                <div class="flex flex-col md:flex-row justify-between items-center">
-                    <div class="flex items-center gap-6 mb-4 md:mb-0">
-                        <a href="https://www.allianceforsustainableenergy.org/" target="_blank" rel="noopener noreferrer">
-                            <img src="{{ url_for('static', filename='images/alliance-logo_black.svg') }}"
-                                 alt="Alliance for Energy Innovation"
-                                 class="h-8">
-                        </a>
-                        <a href="https://www.energy.gov" target="_blank" rel="noopener noreferrer">
-                            <img src="{{ url_for('static', filename='images/doe-logo.svg') }}"
-                                 alt="U.S. Department of Energy"
-                                 class="h-10">
-                        </a>
-                    </div>
-                    <p class="nlr-attr text-center md:text-right max-w-md flex-grow">
-                        The National Laboratory of the Rockies is a national laboratory of the
-                        U.S. Department of Energy, Office of Critical Minerals and Energy Innovation.
-                    </p>
-                </div>
-            </div>
-        </div>
-    </footer>
-
-    <!-- About Modal -->
-    <div id="about-modal" class="fixed inset-0 bg-black bg-opacity-50 hidden z-50 flex items-center justify-center">
-        <div class="bg-white rounded-lg shadow-xl max-w-sm w-full mx-4 overflow-hidden">
-            <!-- Modal Header -->
-            <div class="bg-nlr-blue text-white px-6 py-4 flex justify-between items-center">
-                <h2 class="text-lg font-semibold">About</h2>
-                <button data-action="close-about" class="text-white hover:text-gray-200">
-                    <svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M6 18L18 6M6 6l12 12"/>
-                    </svg>
-                </button>
-            </div>
-
-            <!-- Modal Body -->
-            <div class="px-6 py-5">
-                <div class="p-3 bg-gray-50 rounded">
-                    <div class="flex justify-between items-center">
-                        <span class="text-sm text-gray-500">Version</span>
-                        <span id="about-version" class="font-mono text-sm font-semibold">loading...</span>
-                    </div>
-                    <div class="flex justify-between items-center mt-2">
-                        <span class="text-sm text-gray-500">Commit</span>
-                        <span id="about-commit" class="font-mono text-sm text-gray-600">-</span>
-                    </div>
-                    <div class="flex justify-between items-center mt-2">
-                        <span class="text-sm text-gray-500">Branch</span>
-                        <span id="about-branch" class="font-mono text-sm text-gray-600">-</span>
-                    </div>
-                </div>
-            </div>
-
-            <!-- Modal Footer -->
-            <div class="bg-gray-50 px-6 py-3 flex justify-end">
-                <button data-action="close-about"
-                        class="px-4 py-2 bg-nlr-gray text-white rounded hover:bg-opacity-90 text-sm">
-                    Close
-                </button>
-            </div>
-        </div>
-    </div>
-
-    <!-- Application JavaScript -->
-    <script type="module" src="{{ url_for('static', filename='js/app.js') }}"></script>
-
-    {% block scripts %}{% endblock %}
-</body>
-</html>
diff --git a/app/templates/files.html b/app/templates/files.html
deleted file mode 100644
index 4330026..0000000
--- a/app/templates/files.html
+++ /dev/null
@@ -1,106 +0,0 @@
-{% extends "base.html" %}
-{% from "macros.html" import spinner %}
-
-{% block title %}Browse Uploaded Files - {{ super() }}{% endblock %}
-
-{% block body_attrs %}data-page="files"{% endblock %}
-
-{% block content %}
-<div class="space-y-6">
-    <!-- Header -->
-    <div class="flex items-center justify-between">
-        <div>
-            <h1 class="text-2xl font-bold text-gray-900">S3 File Browser</h1>
-            <p class="text-gray-600 mt-1">Browse uploaded MCAP files in S3</p>
-        </div>
-        <div class="flex items-center space-x-4">
-            <!-- Search -->
-            <div class="relative">
-                <input type="text" id="search-input" placeholder="Search files..."
-                       class="pl-10 pr-4 py-2 border border-gray-300 rounded-md focus:ring-nlr-blue focus:border-nlr-blue">
-                <svg class="absolute left-3 top-2.5 h-5 w-5 text-gray-400" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                    <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2"
-                          d="M21 21l-6-6m2-5a7 7 0 11-14 0 7 7 0 0114 0z" />
-                </svg>
-            </div>
-            <button id="refresh-btn"
-                    class="px-4 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light transition-colors">
-                Refresh
-            </button>
-        </div>
-    </div>
-
-    <!-- Bucket Info -->
-    <div id="bucket-info" class="bg-white rounded-lg shadow p-4">
-        <div class="flex items-center justify-between">
-            <div class="flex items-center space-x-3">
-                <svg class="h-6 w-6 text-nlr-blue" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                    <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2"
-                          d="M4 7v10c0 2.21 3.582 4 8 4s8-1.79 8-4V7M4 7c0 2.21 3.582 4 8 4s8-1.79 8-4M4 7c0-2.21 3.582-4 8-4s8 1.79 8 4" />
-                </svg>
-                <span id="bucket-name" class="font-medium text-gray-900">Loading...</span>
-            </div>
-            <div id="bucket-status" class="text-sm text-gray-500">
-                <!-- Connection status will be shown here -->
-            </div>
-        </div>
-    </div>
-
-    <!-- Breadcrumb Navigation -->
-    <nav id="breadcrumb" class="flex items-center space-x-2 text-sm">
-        <a href="#" data-prefix="" class="text-nlr-blue hover:underline">Root</a>
-        <!-- Breadcrumb items will be inserted here -->
-    </nav>
-
-    <!-- File Browser -->
-    <div class="bg-white rounded-lg shadow overflow-hidden">
-        <!-- Loading State -->
-        <div id="loading-state" class="p-8 text-center">
-            {{ spinner("Loading files...") }}
-        </div>
-
-        <!-- Error State -->
-        <div id="error-state" class="hidden p-8 text-center">
-            <svg class="h-12 w-12 mx-auto text-red-500" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2"
-                      d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z" />
-            </svg>
-            <p id="error-message" class="mt-2 text-red-600">An error occurred</p>
-            <button id="retry-btn"
-                    class="mt-4 px-4 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light transition-colors">
-                Retry
-            </button>
-        </div>
-
-        <!-- Empty State -->
-        <div id="empty-state" class="hidden p-8 text-center">
-            <svg class="h-12 w-12 mx-auto text-gray-400" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2"
-                      d="M3 7v10a2 2 0 002 2h14a2 2 0 002-2V9a2 2 0 00-2-2h-6l-2-2H5a2 2 0 00-2 2z" />
-            </svg>
-            <p class="mt-2 text-gray-600">No files found in this location</p>
-        </div>
-
-        <!-- File List -->
-        <div id="file-list" class="hidden divide-y divide-gray-200">
-            <!-- Folder items will be inserted here -->
-        </div>
-    </div>
-
-    <!-- Search Results -->
-    <div id="search-results" class="hidden bg-white rounded-lg shadow overflow-hidden">
-        <div class="px-6 py-4 border-b border-gray-200 flex items-center justify-between">
-            <h2 class="text-lg font-semibold text-gray-900">Search Results</h2>
-            <button id="close-search-btn" class="text-gray-500 hover:text-gray-700">
-                <svg class="h-5 w-5" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                    <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M6 18L18 6M6 6l12 12" />
-                </svg>
-            </button>
-        </div>
-        <div id="search-results-list" class="divide-y divide-gray-200 max-h-96 overflow-y-auto">
-            <!-- Search results will be inserted here -->
-        </div>
-    </div>
-</div>
-{% endblock %}
-
diff --git a/app/templates/index.html b/app/templates/index.html
deleted file mode 100644
index 4549e2f..0000000
--- a/app/templates/index.html
+++ /dev/null
@@ -1,430 +0,0 @@
-{% extends "base.html" %}
-{% from "macros.html" import spinner, stat_card %}
-
-{% block title %}Upload Files - {{ super() }}{% endblock %}
-
-{% block body_attrs %}data-page="upload"{% endblock %}
-
-{% block content %}
-<div class="space-y-6">
-    <!-- Header -->
-    <div class="flex items-center justify-between">
-        <div>
-            <h1 class="text-2xl font-bold text-gray-900">Upload MCAP Files</h1>
-            <p class="text-gray-600 mt-1">Select a folder to upload MCAP files to MODAQ Cloud (NLR AWS S3)</p>
-        </div>
-    </div>
-
-    <!-- Upload Steps Indicator -->
-    <div id="upload-steps">
-        <div class="bg-white rounded-lg shadow px-6 py-4">
-            <div class="flex items-center justify-between">
-                <!-- Step 1: Select -->
-                <div class="flex items-center cursor-pointer hover:opacity-80" data-step="1" data-action="go-to-step" title="Go back to file selection">
-                    <div class="step-circle flex items-center justify-center w-8 h-8 rounded-full border-2 border-gray-300 bg-white text-gray-500 font-semibold text-sm">
-                        1
-                    </div>
-                    <span class="step-label ml-2 text-sm font-medium text-gray-500">Select</span>
-                </div>
-
-                <!-- Connector -->
-                <div class="step-connector flex-1 h-0.5 bg-gray-300 mx-3"></div>
-
-                <!-- Step 2: Review -->
-                <div class="flex items-center" data-step="2">
-                    <div class="step-circle flex items-center justify-center w-8 h-8 rounded-full border-2 border-gray-300 bg-white text-gray-500 font-semibold text-sm">
-                        2
-                    </div>
-                    <span class="step-label ml-2 text-sm font-medium text-gray-500">Review</span>
-                </div>
-
-                <!-- Connector -->
-                <div class="step-connector flex-1 h-0.5 bg-gray-300 mx-3"></div>
-
-                <!-- Step 3: Upload -->
-                <div class="flex items-center" data-step="3">
-                    <div class="step-circle flex items-center justify-center w-8 h-8 rounded-full border-2 border-gray-300 bg-white text-gray-500 font-semibold text-sm">
-                        3
-                    </div>
-                    <span class="step-label ml-2 text-sm font-medium text-gray-500">Upload</span>
-                </div>
-
-                <!-- Connector -->
-                <div class="step-connector flex-1 h-0.5 bg-gray-300 mx-3"></div>
-
-                <!-- Step 4: Complete -->
-                <div class="flex items-center" data-step="4">
-                    <div class="step-circle flex items-center justify-center w-8 h-8 rounded-full border-2 border-gray-300 bg-white text-gray-500 font-semibold text-sm">
-                        <svg class="w-4 h-4" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7" />
-                        </svg>
-                    </div>
-                    <span class="step-label ml-2 text-sm font-medium text-gray-500">Complete</span>
-                </div>
-            </div>
-
-            <!-- Step Description -->
-            <div id="step-description" class="mt-3 text-center text-sm text-gray-600">
-                Select files or a folder to upload
-            </div>
-        </div>
-    </div>
-
-    <!-- Inline Folder Browser -->
-    <div id="folder-browser-panel" class="bg-white rounded-lg shadow overflow-hidden">
-        <!-- Quick Links -->
-        <div id="folder-quick-links" class="px-6 py-2 bg-gray-50 border-b border-gray-200 flex items-center space-x-2 overflow-x-auto">
-            <!-- Quick links will be inserted here -->
-        </div>
-
-        <!-- Breadcrumb Navigation -->
-        <div class="px-6 py-2 bg-gray-50 border-b border-gray-200">
-            <div id="folder-breadcrumb" class="flex items-center space-x-1 text-sm overflow-x-auto">
-                <!-- Breadcrumbs will be inserted here -->
-            </div>
-        </div>
-
-        <!-- Current Path Info -->
-        <div class="px-6 py-2 bg-blue-50 border-b border-gray-200 flex items-center justify-between">
-            <span class="text-sm text-blue-800" title="Does not include files in subfolders">
-                <span id="folder-mcap-count">0</span> MCAP files in this folder (not subfolders)
-                <span id="browser-root-upload-status" class="ml-2"></span>
-            </span>
-        </div>
-
-        <!-- Browser Scan Status Bar -->
-        <div id="browser-scan-status" class="hidden px-6 py-2 bg-green-50 border-b border-gray-200">
-            <div class="flex items-center justify-between">
-                <div class="flex items-center space-x-2">
-                    <svg id="browser-scan-spinner" class="animate-spin h-4 w-4 text-nlr-blue" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
-                        <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
-                        <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
-                    </svg>
-                    <span id="browser-scan-text" class="text-sm text-gray-700">
-                        Scanning folders...
-                    </span>
-                </div>
-                <label class="flex items-center">
-                    <input type="checkbox" id="browser-hide-uploaded"
-                           class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
-                    <span class="ml-2 text-sm text-gray-600">Hide uploaded folders</span>
-                </label>
-            </div>
-        </div>
-
-        <!-- Folder List (subfolders) -->
-        <div id="folder-list" class="divide-y divide-gray-200">
-            <!-- Folders will be inserted here -->
-        </div>
-
-        <!-- File Table (MCAP files with sortable columns) -->
-        <div id="file-table-section" class="hidden">
-            <table class="w-full divide-y divide-gray-200">
-                <thead class="bg-gray-50" id="file-table-head">
-                    <tr>
-                        <th class="px-6 py-2 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100"
-                            data-file-sort="name">
-                            Filename <span class="file-sort-indicator"></span>
-                        </th>
-                        <th class="px-4 py-2 text-left text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100 w-40"
-                            data-file-sort="mtime">
-                            Date Modified <span class="file-sort-indicator"></span>
-                        </th>
-                        <th class="px-4 py-2 text-right text-xs font-medium text-gray-500 uppercase tracking-wider cursor-pointer hover:bg-gray-100 w-24"
-                            data-file-sort="size">
-                            Size <span class="file-sort-indicator"></span>
-                        </th>
-                    </tr>
-                </thead>
-                <tbody id="file-table-body" class="bg-white divide-y divide-gray-200">
-                    <!-- File rows will be inserted here -->
-                </tbody>
-            </table>
-        </div>
-
-        <!-- Loading State -->
-        <div id="folder-loading" class="hidden p-8 text-center">
-            {{ spinner() }}
-        </div>
-
-        <!-- Error State -->
-        <div id="folder-error" class="hidden p-8 text-center">
-            <p class="text-red-600" id="folder-error-message">Error loading folder</p>
-        </div>
-
-        <!-- Primary Upload Folder Action (sticky so it's visible with large file lists) -->
-        <div class="px-6 py-4 border-t border-gray-200 bg-white sticky bottom-0 flex items-center justify-between">
-            <span id="folder-select-summary" class="text-sm text-gray-600">
-                Navigate to the folder containing your MCAP files, then click Upload Folder.
-            </span>
-            <button id="select-folder-btn"
-                    class="px-8 py-3 bg-nlr-blue text-white text-base font-semibold rounded-lg shadow-md hover:bg-nlr-blue-light transition-colors disabled:bg-gray-300 disabled:text-gray-500 disabled:shadow-none disabled:cursor-not-allowed flex items-center">
-                <span>Upload This Folder</span>
-                <svg class="w-5 h-5 ml-2" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                    <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 7l5 5m0 0l-5 5m5-5H6" />
-                </svg>
-            </button>
-        </div>
-    </div>
-
-    <!-- Scan Results (Step 2: Review) -->
-    <div id="scan-results-section" class="hidden">
-        <div class="bg-white rounded-lg shadow overflow-hidden">
-            <div class="px-6 py-4 border-b border-gray-200">
-                <h2 class="text-lg font-semibold text-gray-900">Review Selected Files</h2>
-                <p class="text-sm text-gray-500 mt-1" id="selected-folder-path"></p>
-            </div>
-
-            <div class="p-6 border-b border-gray-200">
-                <div class="grid grid-cols-3 gap-4 text-center mb-6">
-                    {{ stat_card("scan-total", "Total MCAP Files", "gray") }}
-                    {{ stat_card("scan-total-volume", "Total Volume", "blue", "0 B") }}
-                    {{ stat_card("scan-already-uploaded", "Already Uploaded", "yellow") }}
-                </div>
-
-                <!-- Scan Progress Indicator -->
-                <div id="scan-progress-container" class="hidden mb-4">
-                    <div class="flex items-center space-x-3 px-4 py-3 bg-blue-50 rounded-lg">
-                        <svg class="animate-spin h-5 w-5 text-nlr-blue" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
-                            <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
-                            <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
-                        </svg>
-                        <span id="scan-progress-text" class="text-sm text-blue-800">
-                            Scanning folders...
-                        </span>
-                    </div>
-                </div>
-
-                <div class="flex justify-center space-x-4">
-                    <button id="cancel-scan-btn"
-                            class="px-6 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 transition-colors flex items-center">
-                        <svg class="w-4 h-4 mr-2" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M11 17l-5-5m0 0l5-5m-5 5h12" />
-                        </svg>
-                        <span>Back</span>
-                    </button>
-                    <button id="continue-upload-btn"
-                            class="px-6 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light transition-colors disabled:opacity-50 disabled:cursor-not-allowed flex items-center">
-                        <span>Continue</span>
-                        <svg class="w-4 h-4 ml-2" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 7l5 5m0 0l-5 5m5-5H6" />
-                        </svg>
-                    </button>
-                </div>
-            </div>
-
-            <!-- Sortable File Table -->
-            <div class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center justify-between">
-                <span class="text-sm font-medium text-gray-700">Files</span>
-                <div class="flex items-center space-x-4">
-                    <label class="flex items-center">
-                        <input type="checkbox" id="scan-hide-completed-folders"
-                               class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
-                        <span class="ml-2 text-sm text-gray-600">Hide completed folders</span>
-                    </label>
-                    <label class="flex items-center">
-                        <input type="checkbox" id="scan-hide-uploaded"
-                               class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
-                        <span class="ml-2 text-sm text-gray-600">Hide already uploaded</span>
-                    </label>
-                </div>
-            </div>
-            <div class="overflow-x-auto">
-                <table class="w-full divide-y divide-gray-200 table-fixed">
-                    <thead class="bg-gray-50">
-                        <tr>
-                            <th class="w-1/4 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
-                                Filename
-                            </th>
-                            <th class="w-1/4 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
-                                Path
-                            </th>
-                            <th class="w-1/6 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
-                                Date Modified
-                            </th>
-                            <th class="w-20 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
-                                Size
-                            </th>
-                            <th class="w-24 px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
-                                Status
-                            </th>
-                        </tr>
-                    </thead>
-                    <tbody id="scan-file-list" class="bg-white divide-y divide-gray-200">
-                        <!-- File rows will be inserted here -->
-                    </tbody>
-                </table>
-            </div>
-        </div>
-    </div>
-
-    <!-- Combined Upload (Step 3: Validate + Upload) -->
-    <div id="upload-section" class="hidden">
-        <div class="bg-white rounded-lg shadow overflow-hidden">
-            <div class="px-6 py-4 border-b border-gray-200 flex items-center justify-between">
-                <h2 class="text-lg font-semibold text-gray-900">Upload Progress</h2>
-                <button id="cancel-upload-btn"
-                        class="px-4 py-2 bg-red-500 text-white rounded-md hover:bg-red-600 transition-colors">
-                    Cancel Upload
-                </button>
-            </div>
-
-            <!-- Phase Label -->
-            <div id="upload-phase" class="px-6 py-2 bg-blue-50 border-b border-gray-200">
-                <span class="text-sm font-medium text-blue-800" id="upload-phase-label">Validating files...</span>
-            </div>
-
-            <!-- Overall Progress -->
-            <div class="px-6 py-4 border-b border-gray-200">
-                <div class="flex items-center justify-between mb-2">
-                    <span class="text-sm font-medium text-gray-700">
-                        Overall Progress: <span id="progress-percent">0</span>%
-                    </span>
-                    <span class="text-sm text-gray-500">
-                        <span id="files-completed">0</span> / <span id="files-total">0</span> files
-                        (<span id="bytes-uploaded">0 B</span> / <span id="bytes-total">0 B</span>)
-                    </span>
-                </div>
-                <div class="w-full bg-gray-200 rounded-full h-4">
-                    <div id="progress-bar" class="progress-bar bg-nlr-blue h-4 rounded-full" style="width: 0%"></div>
-                </div>
-                <div class="mt-2 text-sm text-gray-500">
-                    ETA: <span id="eta">Calculating...</span>
-                </div>
-            </div>
-
-            <!-- Compact Status Counters -->
-            <div id="upload-status-counters" class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center space-x-4 text-sm">
-                <span class="text-blue-600"><span class="inline-block w-2 h-2 bg-blue-500 rounded-full mr-1 animate-pulse"></span> <span id="upload-count-active">0</span> active</span>
-                <span class="text-green-600">&#10003; <span id="upload-count-completed">0</span> completed</span>
-                <span class="text-yellow-600">&#9193; <span id="upload-count-skipped">0</span> skipped</span>
-                <span class="text-red-600">&#10007; <span id="upload-count-failed">0</span> failed</span>
-                <span class="text-gray-500">&#9203; <span id="upload-count-queued">0</span> queued</span>
-            </div>
-
-            <!-- Active Uploads (only currently processing files, max ~4-8) -->
-            <div id="upload-active-list" class="divide-y divide-gray-200">
-                <!-- Only actively uploading/analyzing files appear here -->
-            </div>
-        </div>
-    </div>
-
-    <!-- Completion Summary (Step 4: Complete) -->
-    <div id="completion-section" class="hidden">
-        <div class="bg-white rounded-lg shadow overflow-hidden">
-            <div class="px-6 py-4 border-b border-gray-200">
-                <h2 class="text-lg font-semibold text-gray-900">Upload Summary</h2>
-            </div>
-
-            <div class="p-6">
-                <!-- File Status Summary -->
-                <div id="completion-summary" class="grid grid-cols-3 gap-6 text-center mb-6">
-                    {{ stat_card("completed-count", "Uploaded", "green", size="3xl") }}
-                    {{ stat_card("skipped-count", "Skipped", "yellow", size="3xl") }}
-                    {{ stat_card("failed-count", "Failed", "red", size="3xl") }}
-                </div>
-
-                <!-- Aggregate Stats -->
-                <div class="bg-gray-50 rounded-lg p-4 mb-6">
-                    <div class="grid grid-cols-4 gap-4 text-center">
-                        <div>
-                            <div id="total-uploaded-size" class="text-xl font-bold text-gray-800">-</div>
-                            <div class="text-xs text-gray-500">Data Uploaded</div>
-                        </div>
-                        <div>
-                            <div id="total-upload-time" class="text-xl font-bold text-gray-800">-</div>
-                            <div class="text-xs text-gray-500">Total Time</div>
-                        </div>
-                        <div>
-                            <div id="avg-upload-speed" class="text-xl font-bold text-gray-800">-</div>
-                            <div class="text-xs text-gray-500">Avg Speed</div>
-                        </div>
-                        <div>
-                            <div id="avg-file-time" class="text-xl font-bold text-gray-800">-</div>
-                            <div class="text-xs text-gray-500">Avg per File</div>
-                        </div>
-                    </div>
-                </div>
-
-                <!-- Action Buttons -->
-                <div class="flex justify-center space-x-4 mb-6">
-                    <button id="upload-more-btn"
-                            class="px-6 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light transition-colors">
-                        Upload More Files
-                    </button>
-                    <button id="download-csv-btn"
-                            class="px-6 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 transition-colors flex items-center">
-                        <svg class="w-4 h-4 mr-2" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 10v6m0 0l-3-3m3 3l3-3m2 8H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z" />
-                        </svg>
-                        Download CSV
-                    </button>
-                    <a href="{{ url_for('main.files') }}"
-                       class="px-6 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 transition-colors">
-                        Browse Uploaded Files
-                    </a>
-                </div>
-            </div>
-
-            <!-- File Details Table (paginated) -->
-            <div class="border-t border-gray-200">
-                <div class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center justify-between">
-                    <span class="text-sm font-medium text-gray-700">File Details</span>
-                    <div id="completion-pagination" class="flex items-center space-x-2 text-sm">
-                        <button id="completion-prev-btn" class="px-3 py-1 bg-gray-200 rounded hover:bg-gray-300 disabled:opacity-50 disabled:cursor-not-allowed" disabled>Prev</button>
-                        <span id="completion-page-info" class="text-gray-600">Page 1 of 1</span>
-                        <button id="completion-next-btn" class="px-3 py-1 bg-gray-200 rounded hover:bg-gray-300 disabled:opacity-50 disabled:cursor-not-allowed" disabled>Next</button>
-                    </div>
-                </div>
-                <div class="overflow-x-auto">
-                    <table class="w-full divide-y divide-gray-200">
-                        <thead class="bg-gray-50">
-                            <tr>
-                                <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">File</th>
-                                <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">S3 Path</th>
-                                <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">Size</th>
-                                <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">Duration</th>
-                                <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">Speed</th>
-                                <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">Status</th>
-                            </tr>
-                        </thead>
-                        <tbody id="completion-file-list" class="bg-white divide-y divide-gray-200">
-                            <!-- File rows will be inserted here -->
-                        </tbody>
-                    </table>
-                </div>
-            </div>
-        </div>
-    </div>
-</div>
-
-<!-- Confirm Upload Modal -->
-<div id="confirm-upload-modal" class="hidden fixed inset-0 z-50 flex items-center justify-center">
-    <div class="fixed inset-0 bg-black bg-opacity-50" data-action="close-confirm-modal"></div>
-    <div class="relative bg-white rounded-lg shadow-xl max-w-md w-full mx-4 p-6">
-        <h3 class="text-lg font-semibold text-gray-900 mb-4">Upload to MODAQ Cloud?</h3>
-        <p class="text-sm text-gray-600 mb-2">
-            <span id="confirm-file-count" class="font-medium">0</span> files
-            (<span id="confirm-total-size" class="font-medium">0 B</span>) will be uploaded.
-        </p>
-        <label class="flex items-center mb-2">
-            <input type="checkbox" id="force-reupload-checkbox"
-                   class="rounded border-gray-300 text-nlr-blue focus:ring-nlr-blue">
-            <span class="ml-2 text-sm text-gray-700">Force reupload already uploaded files</span>
-        </label>
-        <p id="confirm-skip-note" class="text-xs text-gray-500 mb-6">
-            Duplicate files will be automatically skipped.
-        </p>
-        <div class="flex justify-end space-x-3">
-            <button class="px-4 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 transition-colors"
-                    data-action="close-confirm-modal">
-                Cancel
-            </button>
-            <button id="confirm-upload-btn"
-                    class="px-4 py-2 bg-nlr-green text-white rounded-md hover:bg-nlr-green-light transition-colors">
-                Confirm Upload
-            </button>
-        </div>
-    </div>
-</div>
-{% endblock %}
diff --git a/app/templates/logs.html b/app/templates/logs.html
deleted file mode 100644
index c940502..0000000
--- a/app/templates/logs.html
+++ /dev/null
@@ -1,169 +0,0 @@
-{% extends "base.html" %}
-
-{% block title %}Logs - {{ super() }}{% endblock %}
-
-{% block body_attrs %}data-page="logs"{% endblock %}
-
-{% block content %}
-<div class="space-y-6">
-    <!-- Header -->
-    <div>
-        <h1 class="text-2xl font-bold text-gray-900">Application Logs</h1>
-        <p class="text-gray-600 mt-1">View upload activity, analysis results, and system events</p>
-    </div>
-
-    <!-- Stats Bar -->
-    <div class="grid grid-cols-4 gap-4">
-        <div class="bg-white rounded-lg shadow p-4 text-center">
-            <div id="stat-total" class="text-2xl font-bold text-gray-700">-</div>
-            <div class="text-sm text-gray-500">Total Entries</div>
-        </div>
-        <div class="bg-white rounded-lg shadow p-4 text-center">
-            <div id="stat-today" class="text-2xl font-bold text-nlr-blue">-</div>
-            <div class="text-sm text-gray-500">Today</div>
-        </div>
-        <div class="bg-white rounded-lg shadow p-4 text-center">
-            <div id="stat-errors" class="text-2xl font-bold text-red-600">-</div>
-            <div class="text-sm text-gray-500">Errors</div>
-        </div>
-        <div class="bg-white rounded-lg shadow p-4 text-center">
-            <div id="stat-files" class="text-2xl font-bold text-nlr-gray">-</div>
-            <div class="text-sm text-gray-500">Log Files</div>
-        </div>
-    </div>
-
-    <!-- Filter Bar -->
-    <div class="bg-white rounded-lg shadow p-4">
-        <div class="flex flex-wrap items-center gap-3">
-            <!-- Date Picker -->
-            <div>
-                <input type="date" id="filter-date"
-                       class="border border-gray-300 rounded-md px-3 py-2 text-sm focus:ring-nlr-blue focus:border-nlr-blue">
-            </div>
-
-            <!-- Level Dropdown -->
-            <div>
-                <select id="filter-level"
-                        class="border border-gray-300 rounded-md px-3 py-2 text-sm focus:ring-nlr-blue focus:border-nlr-blue">
-                    <option value="">All Levels</option>
-                    <option value="INFO">INFO</option>
-                    <option value="WARNING">WARNING</option>
-                    <option value="ERROR">ERROR</option>
-                </select>
-            </div>
-
-            <!-- Category Dropdown -->
-            <div>
-                <select id="filter-category"
-                        class="border border-gray-300 rounded-md px-3 py-2 text-sm focus:ring-nlr-blue focus:border-nlr-blue">
-                    <option value="">All Categories</option>
-                    <option value="upload">Upload</option>
-                    <option value="analysis">Analysis</option>
-                    <option value="settings">Settings</option>
-                    <option value="app">App</option>
-                    <option value="sync">Sync</option>
-                </select>
-            </div>
-
-            <!-- Search -->
-            <div class="flex-grow">
-                <input type="text" id="filter-search" placeholder="Search messages..."
-                       class="w-full border border-gray-300 rounded-md px-3 py-2 text-sm focus:ring-nlr-blue focus:border-nlr-blue">
-            </div>
-
-            <!-- Action Buttons -->
-            <button id="clear-filters-btn"
-                    class="px-4 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 text-sm transition-colors">
-                Clear
-            </button>
-            <button id="sync-logs-btn"
-                    class="px-4 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light text-sm transition-colors">
-                Sync to S3
-            </button>
-        </div>
-    </div>
-
-    <!-- Upload Summaries -->
-    <div class="bg-white rounded-lg shadow overflow-hidden">
-        <button id="csv-section-toggle"
-                class="w-full px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center justify-between hover:bg-gray-100 transition-colors">
-            <div class="flex items-center gap-2">
-                <svg id="csv-toggle-icon" class="h-4 w-4 text-gray-500 transform transition-transform" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                    <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 5l7 7-7 7" />
-                </svg>
-                <span class="text-sm font-medium text-gray-700">Upload Summaries</span>
-                <span id="csv-count-badge"
-                      class="px-2 py-0.5 text-xs font-medium rounded-full bg-nlr-blue text-white hidden">0</span>
-            </div>
-        </button>
-        <div id="csv-section-body" class="hidden">
-            <div class="overflow-x-auto">
-                <table class="w-full divide-y divide-gray-200">
-                    <thead class="bg-gray-50">
-                        <tr>
-                            <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase w-28">Date</th>
-                            <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase w-20">Time</th>
-                            <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">Filename</th>
-                            <th class="px-4 py-3 text-right text-xs font-medium text-gray-500 uppercase w-32">Actions</th>
-                        </tr>
-                    </thead>
-                    <tbody id="csv-table-body" class="bg-white divide-y divide-gray-200">
-                        <tr>
-                            <td colspan="4" class="px-4 py-6 text-center text-gray-500 text-sm">No upload summaries found</td>
-                        </tr>
-                    </tbody>
-                </table>
-            </div>
-            <!-- CSV Preview Panel -->
-            <div id="csv-preview-panel" class="hidden border-t border-gray-200">
-                <div class="px-6 py-3 bg-gray-50 flex items-center justify-between">
-                    <span id="csv-preview-title" class="text-sm font-medium text-gray-700">Preview</span>
-                    <button id="csv-preview-close"
-                            class="text-gray-400 hover:text-gray-600 text-sm">Close</button>
-                </div>
-                <div id="csv-preview-content" class="overflow-x-auto p-4"></div>
-            </div>
-        </div>
-    </div>
-
-    <!-- Log Table -->
-    <div class="bg-white rounded-lg shadow overflow-hidden">
-        <!-- Table Header -->
-        <div class="px-6 py-3 bg-gray-50 border-b border-gray-200 flex items-center justify-between">
-            <span id="log-count-label" class="text-sm text-gray-600">Loading...</span>
-            <div class="flex items-center gap-2">
-                <button id="prev-page-btn"
-                        class="px-3 py-1 bg-gray-200 text-gray-600 rounded text-sm hover:bg-gray-300 disabled:opacity-50 disabled:cursor-not-allowed"
-                        disabled>
-                    Previous
-                </button>
-                <button id="next-page-btn"
-                        class="px-3 py-1 bg-gray-200 text-gray-600 rounded text-sm hover:bg-gray-300 disabled:opacity-50 disabled:cursor-not-allowed"
-                        disabled>
-                    Next
-                </button>
-            </div>
-        </div>
-
-        <!-- Table -->
-        <div class="overflow-x-auto">
-            <table class="w-full divide-y divide-gray-200">
-                <thead class="bg-gray-50">
-                    <tr>
-                        <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase w-44">Timestamp</th>
-                        <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase w-20">Level</th>
-                        <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase w-24">Category</th>
-                        <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase w-48">Event</th>
-                        <th class="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase">Message</th>
-                    </tr>
-                </thead>
-                <tbody id="log-table-body" class="bg-white divide-y divide-gray-200">
-                    <tr>
-                        <td colspan="5" class="px-4 py-8 text-center text-gray-500">Loading...</td>
-                    </tr>
-                </tbody>
-            </table>
-        </div>
-    </div>
-</div>
-{% endblock %}
diff --git a/app/templates/macros.html b/app/templates/macros.html
deleted file mode 100644
index 117c521..0000000
--- a/app/templates/macros.html
+++ /dev/null
@@ -1,16 +0,0 @@
-{# Reusable template macros #}
-
-{% macro spinner(message="Loading...") %}
-<svg class="spinner h-8 w-8 mx-auto text-nlr-blue" fill="none" viewBox="0 0 24 24">
-    <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
-    <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
-</svg>
-<p class="mt-2 text-gray-500">{{ message }}</p>
-{% endmacro %}
-
-{% macro stat_card(id, label, color, value="0", size="2xl") %}
-<div class="bg-{{ color }}-50 rounded-lg p-4">
-    <div id="{{ id }}" class="text-{{ size }} font-bold text-{{ color }}-600">{{ value }}</div>
-    <div class="text-sm text-{{ color }}-700">{{ label }}</div>
-</div>
-{% endmacro %}
diff --git a/app/templates/settings.html b/app/templates/settings.html
deleted file mode 100644
index 8e61dfd..0000000
--- a/app/templates/settings.html
+++ /dev/null
@@ -1,241 +0,0 @@
-{% extends "base.html" %}
-
-{% block title %}Settings - {{ super() }}{% endblock %}
-
-{% block body_attrs %}data-page="settings"{% endblock %}
-
-{% block content %}
-<div class="space-y-6">
-    <!-- Header -->
-    <div>
-        <h1 class="text-2xl font-bold text-gray-900">Settings</h1>
-        <p class="text-gray-600 mt-1">Configure AWS credentials and S3 bucket</p>
-    </div>
-
-    <!-- Settings Form -->
-    <div class="bg-white rounded-lg shadow overflow-hidden">
-        <form id="settings-form" class="divide-y divide-gray-200">
-            <!-- AWS Profile -->
-            <div class="px-6 py-4">
-                <label for="aws-profile" class="block text-sm font-medium text-gray-700">AWS Profile</label>
-                <select id="aws-profile"
-                        class="mt-1 block w-full pl-3 pr-10 py-2 text-base border-gray-300 focus:outline-none focus:ring-nlr-blue focus:border-nlr-blue rounded-md">
-                    <option value="">Loading profiles...</option>
-                </select>
-                <p class="mt-1 text-sm text-gray-500">Select AWS profile from ~/.aws/credentials</p>
-            </div>
-
-            <!-- AWS Region -->
-            <div class="px-6 py-4">
-                <label for="aws-region-select" class="block text-sm font-medium text-gray-700">AWS Region</label>
-                <select id="aws-region-select"
-                        class="mt-1 block w-full pl-3 pr-10 py-2 text-base border-gray-300 focus:outline-none focus:ring-nlr-blue focus:border-nlr-blue rounded-md">
-                    <option value="us-west-2">US West (Oregon) - us-west-2 (NLR Default)</option>
-                    <option value="us-west-1">US West (N. California) - us-west-1</option>
-                    <option value="us-east-1">US East (N. Virginia) - us-east-1</option>
-                    <option value="us-east-2">US East (Ohio) - us-east-2</option>
-                    <option value="us-gov-west-1">AWS GovCloud (US-West) - us-gov-west-1</option>
-                    <option value="us-gov-east-1">AWS GovCloud (US-East) - us-gov-east-1</option>
-                    <option value="other">Other...</option>
-                </select>
-                <input type="text" id="aws-region-custom"
-                       class="mt-2 block w-full px-3 py-2 border border-gray-300 rounded-md shadow-sm focus:outline-none focus:ring-nlr-blue focus:border-nlr-blue hidden"
-                       placeholder="e.g. eu-west-1">
-                <p id="aws-region-help" class="mt-1 text-sm text-gray-500 hidden">
-                    See <a href="https://docs.aws.amazon.com/global-infrastructure/latest/regions/aws-regions.html"
-                           target="_blank" rel="noopener noreferrer"
-                           class="text-nlr-blue hover:underline">AWS Regions documentation</a> for available regions.
-                </p>
-            </div>
-
-            <!-- S3 Bucket -->
-            <div class="px-6 py-4">
-                <label for="s3-bucket" class="block text-sm font-medium text-gray-700">S3 Bucket</label>
-                <input type="text" id="s3-bucket"
-                       class="mt-1 block w-full px-3 py-2 border border-gray-300 rounded-md shadow-sm focus:outline-none focus:ring-nlr-blue focus:border-nlr-blue"
-                       placeholder="my-mcap-bucket">
-                <p class="mt-1 text-sm text-gray-500">Name of the S3 bucket to upload files to</p>
-            </div>
-
-            <!-- Default Upload Folder -->
-            <div class="px-6 py-4">
-                <label for="default-folder" class="block text-sm font-medium text-gray-700">Default Upload Folder</label>
-                <input type="text" id="default-folder"
-                       class="mt-1 block w-full px-3 py-2 border border-gray-300 rounded-md shadow-sm focus:outline-none focus:ring-nlr-blue focus:border-nlr-blue"
-                       placeholder="/path/to/mcap/files">
-                <p class="mt-1 text-sm text-gray-500">Default folder to open when selecting files (optional)</p>
-            </div>
-
-            <!-- Connection Test -->
-            <div class="px-6 py-4 bg-gray-50">
-                <div class="flex items-center justify-between">
-                    <div>
-                        <span class="text-sm font-medium text-gray-700">Connection Status</span>
-                        <div id="connection-status" class="mt-1 text-sm text-gray-500">
-                            Not tested
-                        </div>
-                    </div>
-                    <button type="button" id="test-connection-btn"
-                            class="px-4 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light transition-colors">
-                        Test Connection
-                    </button>
-                </div>
-            </div>
-
-            <!-- Save Button -->
-            <div class="px-6 py-4 flex justify-end">
-                <button type="submit"
-                        class="px-6 py-2 bg-nlr-green text-white rounded-md hover:bg-nlr-green-light transition-colors">
-                    Save Settings
-                </button>
-            </div>
-        </form>
-    </div>
-
-    <!-- Application Update Section -->
-    <div class="bg-white rounded-lg shadow overflow-hidden">
-        <div class="px-6 py-4 border-b border-gray-200">
-            <h2 class="text-lg font-semibold text-gray-900">Application Updates</h2>
-            <p class="text-gray-600 text-sm mt-1">Download the latest updates from <a
-              href="https://github.com/MODAQ2/modaq_upload">GitHub/MODAQ2</a></p>
-        </div>
-
-        <!-- Version Info -->
-        <div class="px-6 py-4 border-b border-gray-200 bg-gray-50">
-            <div class="grid grid-cols-4 gap-4 text-sm">
-                <div>
-                    <span class="text-gray-500">Version:</span>
-                    <span id="pkg-version" class="ml-2 font-semibold text-nlr-blue">-</span>
-                </div>
-                <div>
-                    <span class="text-gray-500">Branch:</span>
-                    <span id="git-branch" class="ml-2 font-medium text-gray-900">-</span>
-                </div>
-                <div>
-                    <span class="text-gray-500">Commit:</span>
-                    <span id="git-commit" class="ml-2 font-mono text-gray-900">-</span>
-                </div>
-                <div>
-                    <span class="text-gray-500">Last Updated:</span>
-                    <span id="git-date" class="ml-2 text-gray-900">-</span>
-                </div>
-            </div>
-        </div>
-
-        <!-- Update Controls -->
-        <div class="px-6 py-4">
-            <div class="flex items-center justify-between">
-                <div>
-                    <div id="update-status" class="text-sm text-gray-600">
-                        Click "Check for Updates" to see if updates are available
-                    </div>
-                </div>
-                <div class="flex space-x-4">
-                    <button type="button" id="check-updates-btn"
-                            class="px-4 py-2 bg-gray-200 text-gray-700 rounded-md hover:bg-gray-300 transition-colors">
-                        Check for Updates
-                    </button>
-                    <button type="button" id="run-update-btn"
-                            class="px-4 py-2 bg-nlr-yellow text-white rounded-md hover:bg-nlr-yellow-light transition-colors disabled:opacity-50 disabled:cursor-not-allowed"
-                            disabled>
-                        Update Application
-                    </button>
-                </div>
-            </div>
-        </div>
-
-        <!-- Update Log -->
-        <div id="update-log" class="hidden px-6 py-4 border-t border-gray-200">
-            <h3 class="text-sm font-medium text-gray-700 mb-2">Update Log</h3>
-            <pre id="update-output" class="bg-gray-900 text-green-400 p-4 rounded-md text-xs overflow-x-auto max-h-64 overflow-y-auto"></pre>
-        </div>
-    </div>
-
-    <!-- Cache Management Section -->
-    <div class="bg-white rounded-lg shadow overflow-hidden">
-        <div class="px-6 py-4 border-b border-gray-200">
-            <h2 class="text-lg font-semibold text-gray-900">Upload Cache</h2>
-            <p class="text-gray-600 text-sm mt-1">Local cache for tracking uploaded files and detecting duplicates</p>
-        </div>
-
-        <!-- Cache Stats -->
-        <div class="px-6 py-4 border-b border-gray-200 bg-gray-50">
-            <div class="grid grid-cols-4 gap-4 text-sm">
-                <div>
-                    <span class="text-gray-500">Cached Files:</span>
-                    <span id="cache-total" class="ml-2 font-semibold text-gray-900">-</span>
-                </div>
-                <div>
-                    <span class="text-gray-500">Exists:</span>
-                    <span id="cache-exists" class="ml-2 font-medium text-green-600">-</span>
-                </div>
-                <div>
-                    <span class="text-gray-500">Deleted:</span>
-                    <span id="cache-deleted" class="ml-2 font-medium text-red-600">-</span>
-                </div>
-                <div>
-                    <span class="text-gray-500">Last Sync:</span>
-                    <span id="cache-last-sync" class="ml-2 text-gray-900">Never</span>
-                </div>
-            </div>
-        </div>
-
-        <!-- Sync Controls -->
-        <div class="px-6 py-4">
-            <div class="flex items-center justify-between">
-                <div>
-                    <span class="text-sm font-medium text-gray-700">Sync with AWS</span>
-                    <p class="text-sm text-gray-500">Reconcile cache with actual S3 bucket state (marks deleted files)</p>
-                </div>
-                <div class="flex space-x-4">
-                    <button type="button" id="sync-cache-btn"
-                            class="px-4 py-2 bg-nlr-blue text-white rounded-md hover:bg-nlr-blue-light transition-colors">
-                        Sync Cache with AWS
-                    </button>
-                </div>
-            </div>
-            <div id="sync-status" class="mt-2 text-sm text-gray-600 hidden"></div>
-        </div>
-    </div>
-
-    <!-- Danger Zone -->
-    <div class="bg-white rounded-lg shadow overflow-hidden border border-red-200">
-        <div class="px-6 py-4 bg-red-50 border-b border-red-200">
-            <h2 class="text-lg font-semibold text-red-700">Danger Zone</h2>
-        </div>
-        <div class="px-6 py-4 space-y-4">
-            <div class="flex items-center justify-between">
-                <div>
-                    <span class="text-sm font-medium text-gray-700">Clear Browser Cache</span>
-                    <p class="text-sm text-gray-500">Clear remembered folders and local preferences</p>
-                </div>
-                <button type="button" id="clear-cache-btn"
-                        class="px-4 py-2 bg-orange-500 text-white rounded-md hover:bg-orange-600 transition-colors">
-                    Clear Cache
-                </button>
-            </div>
-            <div class="flex items-center justify-between pt-4 border-t border-gray-200">
-                <div>
-                    <span class="text-sm font-medium text-gray-700">Clear Upload Cache</span>
-                    <p class="text-sm text-gray-500">Delete all cached file records for current bucket</p>
-                </div>
-                <button type="button" id="invalidate-cache-btn"
-                        class="px-4 py-2 bg-orange-500 text-white rounded-md hover:bg-orange-600 transition-colors">
-                    Clear Upload Cache
-                </button>
-            </div>
-            <div class="flex items-center justify-between pt-4 border-t border-gray-200">
-                <div>
-                    <span class="text-sm font-medium text-gray-700">Reset Settings</span>
-                    <p class="text-sm text-gray-500">Reset all settings to defaults</p>
-                </div>
-                <button type="button" id="reset-settings-btn"
-                        class="px-4 py-2 bg-red-500 text-white rounded-md hover:bg-red-600 transition-colors">
-                    Reset to Defaults
-                </button>
-            </div>
-        </div>
-    </div>
-</div>
-{% endblock %}
-

From f99be6f120356c9d12dd3e17344efcd9e74c9b87 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 17:03:13 -0700
Subject: [PATCH 095/173] Refactor: Remove migrated assets

---
 app/static/images/alliance-logo_black.svg |  59 ----
 app/static/images/doe-logo.svg            | 339 ----------------------
 app/static/images/modaq-logo.png          | Bin 3833 -> 0 bytes
 app/static/images/nlr-logo@2x-01.png      | Bin 23341 -> 0 bytes
 4 files changed, 398 deletions(-)
 delete mode 100644 app/static/images/alliance-logo_black.svg
 delete mode 100644 app/static/images/doe-logo.svg
 delete mode 100644 app/static/images/modaq-logo.png
 delete mode 100644 app/static/images/nlr-logo@2x-01.png

diff --git a/app/static/images/alliance-logo_black.svg b/app/static/images/alliance-logo_black.svg
deleted file mode 100644
index be59986..0000000
--- a/app/static/images/alliance-logo_black.svg
+++ /dev/null
@@ -1,59 +0,0 @@
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-  <defs>
-    <style>
-      .cls-1 {
-        fill: #cdcdcd;
-      }
-
-      .cls-1, .cls-2, .cls-3 {
-        stroke-width: 0px;
-      }
-
-      .cls-1, .cls-3 {
-        fill-rule: evenodd;
-      }
-
-      .cls-2, .cls-3 {
-        fill: #231f20;
-      }
-    </style>
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\ No newline at end of file
diff --git a/app/static/images/doe-logo.svg b/app/static/images/doe-logo.svg
deleted file mode 100644
index 7075378..0000000
--- a/app/static/images/doe-logo.svg
+++ /dev/null
@@ -1,339 +0,0 @@
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-        stroke: #231f20;
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-
-      .cls-1, .cls-2, .cls-3, .cls-4, .cls-5, .cls-6, .cls-7, .cls-12, .cls-13, .cls-14, .cls-15, .cls-16, .cls-17 {
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-
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From f33de36cdb0e5cc6252270834ea3d00012e69b9b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 17:04:01 -0700
Subject: [PATCH 096/173] Refactor: Remove old js tests

---
 tests/js/file-browser.test.js   |  35 ----------
 tests/js/logs.test.js           |  44 -------------
 tests/js/settings.test.js       |  18 ------
 tests/js/state.test.js          |  39 ------------
 tests/js/stepper.test.js        | 101 -----------------------------
 tests/js/upload-control.test.js |  81 ------------------------
 tests/js/upload-exec.test.js    | 105 ------------------------------
 tests/js/utils.test.js          | 109 --------------------------------
 8 files changed, 532 deletions(-)
 delete mode 100644 tests/js/file-browser.test.js
 delete mode 100644 tests/js/logs.test.js
 delete mode 100644 tests/js/settings.test.js
 delete mode 100644 tests/js/state.test.js
 delete mode 100644 tests/js/stepper.test.js
 delete mode 100644 tests/js/upload-control.test.js
 delete mode 100644 tests/js/upload-exec.test.js
 delete mode 100644 tests/js/utils.test.js

diff --git a/tests/js/file-browser.test.js b/tests/js/file-browser.test.js
deleted file mode 100644
index c9b9ebb..0000000
--- a/tests/js/file-browser.test.js
+++ /dev/null
@@ -1,35 +0,0 @@
-import { describe, it, expect, beforeEach, vi } from 'vitest';
-import state from '../../app/static/js/modules/state.js';
-
-describe('file-browser', () => {
-    beforeEach(() => {
-        state.currentPrefix = '';
-
-        document.body.innerHTML = `
-            <div id="refresh-btn"></div>
-            <input id="search-input" type="text" />
-            <div id="retry-btn"></div>
-            <div id="close-search-btn"></div>
-            <div id="bucket-name">Loading...</div>
-            <div id="bucket-status"></div>
-            <div id="loading-state" class="hidden"></div>
-            <div id="error-state" class="hidden"></div>
-            <div id="error-message"></div>
-            <div id="empty-state" class="hidden"></div>
-            <div id="file-list" class="hidden"></div>
-            <nav id="breadcrumb"></nav>
-            <div id="search-results" class="hidden"></div>
-            <div id="search-results-list"></div>
-        `;
-    });
-
-    it('state.currentPrefix defaults to empty string', () => {
-        expect(state.currentPrefix).toBe('');
-    });
-
-    it('currentPrefix can be updated', () => {
-        state.currentPrefix = 'year=2024/';
-        expect(state.currentPrefix).toBe('year=2024/');
-        state.currentPrefix = '';
-    });
-});
diff --git a/tests/js/logs.test.js b/tests/js/logs.test.js
deleted file mode 100644
index c69cb18..0000000
--- a/tests/js/logs.test.js
+++ /dev/null
@@ -1,44 +0,0 @@
-import { describe, it, expect, beforeEach } from 'vitest';
-import state from '../../app/static/js/modules/state.js';
-
-describe('logs state', () => {
-  beforeEach(() => {
-    state.logFilters = { date: null, level: null, category: null, search: '' };
-    state.logPagination = { offset: 0, limit: 100 };
-  });
-
-  it('logFilters defaults are correct', () => {
-    expect(state.logFilters.date).toBeNull();
-    expect(state.logFilters.level).toBeNull();
-    expect(state.logFilters.category).toBeNull();
-    expect(state.logFilters.search).toBe('');
-  });
-
-  it('logPagination defaults are correct', () => {
-    expect(state.logPagination.offset).toBe(0);
-    expect(state.logPagination.limit).toBe(100);
-  });
-
-  it('logFilters can be updated', () => {
-    state.logFilters.date = '2026-02-07';
-    state.logFilters.level = 'ERROR';
-    state.logFilters.category = 'upload';
-    state.logFilters.search = 'test';
-
-    expect(state.logFilters.date).toBe('2026-02-07');
-    expect(state.logFilters.level).toBe('ERROR');
-    expect(state.logFilters.category).toBe('upload');
-    expect(state.logFilters.search).toBe('test');
-  });
-
-  it('logPagination offset can be advanced', () => {
-    state.logPagination.offset = 100;
-    expect(state.logPagination.offset).toBe(100);
-  });
-
-  it('logFilters can be reset', () => {
-    state.logFilters.level = 'ERROR';
-    state.logFilters = { date: null, level: null, category: null, search: '' };
-    expect(state.logFilters.level).toBeNull();
-  });
-});
diff --git a/tests/js/settings.test.js b/tests/js/settings.test.js
deleted file mode 100644
index 534e0ff..0000000
--- a/tests/js/settings.test.js
+++ /dev/null
@@ -1,18 +0,0 @@
-import { describe, it, expect, beforeEach } from 'vitest';
-import state from '../../app/static/js/modules/state.js';
-
-describe('settings', () => {
-    beforeEach(() => {
-        state.currentAwsProfile = undefined;
-    });
-
-    it('state.currentAwsProfile defaults to undefined', () => {
-        expect(state.currentAwsProfile).toBeUndefined();
-    });
-
-    it('state.currentAwsProfile can be set', () => {
-        state.currentAwsProfile = 'my-profile';
-        expect(state.currentAwsProfile).toBe('my-profile');
-        state.currentAwsProfile = undefined;
-    });
-});
diff --git a/tests/js/state.test.js b/tests/js/state.test.js
deleted file mode 100644
index 3a04e2a..0000000
--- a/tests/js/state.test.js
+++ /dev/null
@@ -1,39 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import state from '../../app/static/js/modules/state.js';
-
-describe('state', () => {
-    it('has correct default values', () => {
-        expect(state.currentJobId).toBeNull();
-        expect(state.eventSource).toBeNull();
-        expect(state.selectedFolderPath).toBeNull();
-        expect(state.currentStep).toBe(1);
-        expect(state.currentPrefix).toBe('');
-        expect(state.appVersionData).toBeNull();
-        expect(state.currentAwsProfile).toBeUndefined();
-        expect(state.scanFilePaths).toEqual([]);
-        expect(state.scanFileStatuses).toEqual([]);
-        expect(state.scanTotalSize).toBe(0);
-        expect(state.scanFolderPath).toBeNull();
-        expect(state.reviewSortConfig).toEqual({ column: 'filename', ascending: true });
-    });
-
-    it('is a shared mutable reference', () => {
-        const originalStep = state.currentStep;
-        state.currentStep = 3;
-        expect(state.currentStep).toBe(3);
-        state.currentStep = originalStep;
-    });
-
-    it('allows setting and clearing job id', () => {
-        state.currentJobId = 'test-job-123';
-        expect(state.currentJobId).toBe('test-job-123');
-        state.currentJobId = null;
-        expect(state.currentJobId).toBeNull();
-    });
-
-    it('allows managing scan file paths', () => {
-        state.scanFilePaths = ['/path/to/file1.mcap', '/path/to/file2.mcap'];
-        expect(state.scanFilePaths).toHaveLength(2);
-        state.scanFilePaths = [];
-    });
-});
diff --git a/tests/js/stepper.test.js b/tests/js/stepper.test.js
deleted file mode 100644
index 5e1416d..0000000
--- a/tests/js/stepper.test.js
+++ /dev/null
@@ -1,101 +0,0 @@
-import { describe, it, expect, beforeEach } from 'vitest';
-import { setUploadStep, showUploadSteps, hideUploadSteps, goToStep } from '../../app/static/js/modules/stepper.js';
-import state from '../../app/static/js/modules/state.js';
-
-describe('stepper', () => {
-    beforeEach(() => {
-        state.currentStep = 1;
-
-        document.body.innerHTML = `
-            <div id="upload-steps">
-                <div data-step="1" class=""><div class="step-circle"></div><span class="step-label"></span></div>
-                <div class="step-connector"></div>
-                <div data-step="2" class=""><div class="step-circle"></div><span class="step-label"></span></div>
-                <div class="step-connector"></div>
-                <div data-step="3" class=""><div class="step-circle"></div><span class="step-label"></span></div>
-                <div class="step-connector"></div>
-                <div data-step="4" class=""><div class="step-circle"></div><span class="step-label"></span></div>
-            </div>
-            <div id="step-description"></div>
-        `;
-    });
-
-    describe('setUploadStep', () => {
-        it('sets the active step', () => {
-            setUploadStep(3);
-
-            const step3 = document.querySelector('[data-step="3"]');
-            expect(step3.classList.contains('active')).toBe(true);
-            expect(step3.classList.contains('completed')).toBe(false);
-        });
-
-        it('marks previous steps as completed', () => {
-            setUploadStep(3);
-
-            const step1 = document.querySelector('[data-step="1"]');
-            const step2 = document.querySelector('[data-step="2"]');
-            expect(step1.classList.contains('completed')).toBe(true);
-            expect(step2.classList.contains('completed')).toBe(true);
-        });
-
-        it('leaves future steps unmarked', () => {
-            setUploadStep(3);
-
-            const step4 = document.querySelector('[data-step="4"]');
-            expect(step4.classList.contains('active')).toBe(false);
-            expect(step4.classList.contains('completed')).toBe(false);
-        });
-
-        it('updates the step description', () => {
-            setUploadStep(1);
-            const desc = document.getElementById('step-description');
-            expect(desc.textContent).toBe('Select files or a folder to upload');
-        });
-
-        it('updates state.currentStep', () => {
-            setUploadStep(4);
-            expect(state.currentStep).toBe(4);
-        });
-
-        it('colors connectors for completed steps', () => {
-            setUploadStep(3);
-            const connectors = document.querySelectorAll('.step-connector');
-            expect(connectors[0].style.backgroundColor).toBe('rgb(93, 151, 50)');
-            expect(connectors[1].style.backgroundColor).toBe('rgb(93, 151, 50)');
-            expect(connectors[2].style.backgroundColor).toBe('rgb(209, 213, 219)');
-        });
-    });
-
-    describe('showUploadSteps', () => {
-        it('delegates to setUploadStep', () => {
-            showUploadSteps(2);
-            expect(state.currentStep).toBe(2);
-            const step2 = document.querySelector('[data-step="2"]');
-            expect(step2.classList.contains('active')).toBe(true);
-        });
-    });
-
-    describe('hideUploadSteps', () => {
-        it('resets to step 1', () => {
-            setUploadStep(4);
-            hideUploadSteps();
-            expect(state.currentStep).toBe(1);
-            const step1 = document.querySelector('[data-step="1"]');
-            expect(step1.classList.contains('active')).toBe(true);
-        });
-    });
-
-    describe('goToStep', () => {
-        it('does nothing when navigating forward', async () => {
-            state.currentStep = 2;
-            await goToStep(3);
-            expect(state.currentStep).toBe(2);
-        });
-
-        it('does nothing when navigating to current step', async () => {
-            state.currentStep = 2;
-            await goToStep(2);
-            expect(state.currentStep).toBe(2);
-        });
-    });
-});
diff --git a/tests/js/upload-control.test.js b/tests/js/upload-control.test.js
deleted file mode 100644
index 401e366..0000000
--- a/tests/js/upload-control.test.js
+++ /dev/null
@@ -1,81 +0,0 @@
-import { describe, it, expect, beforeEach } from 'vitest';
-import { resetUpload } from '../../app/static/js/modules/upload-control.js';
-import state from '../../app/static/js/modules/state.js';
-
-describe('upload-control', () => {
-    beforeEach(() => {
-        state.currentJobId = 'test-job';
-        state.eventSource = null;
-        state.selectedFolderPath = '/some/path';
-        state.scanFilePaths = ['/file1.mcap'];
-        state.scanFileStatuses = [{ path: '/file1.mcap', filename: 'file1.mcap', size: 100, already_uploaded: false }];
-        state.scanTotalSize = 100;
-        state.scanFolderPath = '/some/path';
-        state.currentStep = 3;
-
-        document.body.innerHTML = `
-            <div id="upload-steps">
-                <div data-step="1"></div>
-                <div class="step-connector"></div>
-                <div data-step="2"></div>
-                <div class="step-connector"></div>
-                <div data-step="3"></div>
-                <div class="step-connector"></div>
-                <div data-step="4"></div>
-            </div>
-            <div id="step-description"></div>
-            <div id="folder-browser-panel" class="hidden"></div>
-            <div id="upload-section"></div>
-            <div id="completion-section"></div>
-            <div id="scan-results-section"></div>
-            <div id="confirm-upload-modal"></div>
-        `;
-    });
-
-    describe('resetUpload', () => {
-        it('clears the job ID', () => {
-            resetUpload();
-            expect(state.currentJobId).toBeNull();
-        });
-
-        it('clears selected folder path', () => {
-            resetUpload();
-            expect(state.selectedFolderPath).toBeNull();
-        });
-
-        it('clears scan file paths', () => {
-            resetUpload();
-            expect(state.scanFilePaths).toEqual([]);
-        });
-
-        it('clears scan file statuses and total size', () => {
-            resetUpload();
-            expect(state.scanFileStatuses).toEqual([]);
-            expect(state.scanTotalSize).toBe(0);
-            expect(state.scanFolderPath).toBeNull();
-        });
-
-        it('shows folder browser panel and hides other sections', () => {
-            resetUpload();
-
-            expect(document.getElementById('folder-browser-panel').classList.contains('hidden')).toBe(false);
-            expect(document.getElementById('upload-section').classList.contains('hidden')).toBe(true);
-            expect(document.getElementById('completion-section').classList.contains('hidden')).toBe(true);
-            expect(document.getElementById('scan-results-section').classList.contains('hidden')).toBe(true);
-            expect(document.getElementById('confirm-upload-modal').classList.contains('hidden')).toBe(true);
-        });
-
-        it('resets stepper to step 1', () => {
-            resetUpload();
-            expect(state.currentStep).toBe(1);
-        });
-
-        it('closes eventSource if open', () => {
-            let closeCalled = false;
-            state.eventSource = { close: () => { closeCalled = true; } };
-            resetUpload();
-            expect(closeCalled).toBe(true);
-            expect(state.eventSource).toBeNull();
-        });
-    });
-});
diff --git a/tests/js/upload-exec.test.js b/tests/js/upload-exec.test.js
deleted file mode 100644
index a1262d8..0000000
--- a/tests/js/upload-exec.test.js
+++ /dev/null
@@ -1,105 +0,0 @@
-import { describe, it, expect, beforeEach } from 'vitest';
-import { updateProgressUI, showCompletionSummary } from '../../app/static/js/modules/upload-exec.js';
-import state from '../../app/static/js/modules/state.js';
-
-describe('upload-exec', () => {
-    beforeEach(() => {
-        state.currentStep = 3;
-
-        document.body.innerHTML = `
-            <div id="upload-steps">
-                <div data-step="1"></div>
-                <div class="step-connector"></div>
-                <div data-step="2"></div>
-                <div class="step-connector"></div>
-                <div data-step="3"></div>
-                <div class="step-connector"></div>
-                <div data-step="4"></div>
-            </div>
-            <div id="step-description"></div>
-            <div id="progress-percent"></div>
-            <div id="progress-bar" style="width: 0%"></div>
-            <div id="files-completed"></div>
-            <div id="files-total"></div>
-            <div id="bytes-uploaded"></div>
-            <div id="bytes-total"></div>
-            <div id="eta"></div>
-            <div id="upload-section"></div>
-            <div id="completion-section" class="hidden"></div>
-            <div id="completed-count"></div>
-            <div id="skipped-count"></div>
-            <div id="failed-count"></div>
-            <div id="total-uploaded-size"></div>
-            <div id="total-upload-time"></div>
-            <div id="avg-upload-speed"></div>
-            <div id="avg-file-time"></div>
-            <div id="completion-file-list"></div>
-        `;
-    });
-
-    describe('updateProgressUI', () => {
-        it('updates progress elements', () => {
-            updateProgressUI({
-                progress_percent: 50.5,
-                files_completed: 3,
-                total_files: 6,
-                uploaded_bytes_formatted: '15 MB',
-                total_bytes_formatted: '30 MB',
-                eta_seconds: 120,
-                files: [
-                    { filename: 'test.mcap', status: 'completed', file_size_formatted: '5 MB', progress_percent: 100 },
-                    { filename: 'test2.mcap', status: 'uploading', file_size_formatted: '5 MB', progress_percent: 50 },
-                ],
-            });
-
-            expect(document.getElementById('progress-percent').textContent).toBe('50.5');
-            expect(document.getElementById('files-completed').textContent).toBe('3');
-            expect(document.getElementById('files-total').textContent).toBe('6');
-            expect(document.getElementById('bytes-uploaded').textContent).toBe('15 MB');
-            expect(document.getElementById('bytes-total').textContent).toBe('30 MB');
-            expect(document.getElementById('eta').textContent).toBe('2m 0s');
-        });
-    });
-
-    describe('showCompletionSummary', () => {
-        it('updates completion counts', () => {
-            showCompletionSummary({
-                files: [
-                    { status: 'completed', filename: 'a.mcap', file_size_formatted: '5 MB' },
-                    { status: 'completed', filename: 'b.mcap', file_size_formatted: '3 MB' },
-                    { status: 'skipped', filename: 'c.mcap', file_size_formatted: '2 MB' },
-                    { status: 'failed', filename: 'd.mcap', file_size_formatted: '1 MB' },
-                ],
-                files_uploaded: 2,
-                files_skipped: 1,
-                files_failed: 1,
-                successfully_uploaded_bytes_formatted: '8 MB',
-                total_upload_duration_formatted: '1m 30s',
-                average_upload_speed_mbps: 42.5,
-            });
-
-            expect(document.getElementById('completed-count').textContent).toBe('2');
-            expect(document.getElementById('skipped-count').textContent).toBe('1');
-            expect(document.getElementById('failed-count').textContent).toBe('1');
-            expect(document.getElementById('total-uploaded-size').textContent).toBe('8 MB');
-            expect(document.getElementById('avg-upload-speed').textContent).toBe('42.5 Mbps');
-        });
-
-        it('sets step to 4 (complete)', () => {
-            showCompletionSummary({
-                files: [{ status: 'completed', filename: 'a.mcap', file_size_formatted: '5 MB' }],
-            });
-
-            expect(state.currentStep).toBe(4);
-        });
-
-        it('shows completion section and hides upload section', () => {
-            showCompletionSummary({
-                files: [{ status: 'completed', filename: 'a.mcap', file_size_formatted: '5 MB' }],
-            });
-
-            expect(document.getElementById('upload-section').classList.contains('hidden')).toBe(true);
-            expect(document.getElementById('completion-section').classList.contains('hidden')).toBe(false);
-        });
-    });
-});
diff --git a/tests/js/utils.test.js b/tests/js/utils.test.js
deleted file mode 100644
index 45070b7..0000000
--- a/tests/js/utils.test.js
+++ /dev/null
@@ -1,109 +0,0 @@
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { showNotification } from '../../app/static/js/modules/notify.js';
-import { formatBytes, formatEta, formatDuration } from '../../app/static/js/modules/formatters.js';
-
-describe('formatBytes', () => {
-    it('returns "0 B" for zero bytes', () => {
-        expect(formatBytes(0)).toBe('0 B');
-    });
-
-    it('formats bytes correctly', () => {
-        expect(formatBytes(500)).toBe('500 B');
-    });
-
-    it('formats kilobytes', () => {
-        expect(formatBytes(1024)).toBe('1 KB');
-        expect(formatBytes(1536)).toBe('1.5 KB');
-    });
-
-    it('formats megabytes', () => {
-        expect(formatBytes(1048576)).toBe('1 MB');
-        expect(formatBytes(1572864)).toBe('1.5 MB');
-    });
-
-    it('formats gigabytes', () => {
-        expect(formatBytes(1073741824)).toBe('1 GB');
-    });
-
-    it('formats terabytes', () => {
-        expect(formatBytes(1099511627776)).toBe('1 TB');
-    });
-});
-
-describe('formatEta', () => {
-    it('returns "Calculating..." for null/undefined', () => {
-        expect(formatEta(null)).toBe('Calculating...');
-        expect(formatEta(undefined)).toBe('Calculating...');
-    });
-
-    it('returns "Calculating..." for negative values', () => {
-        expect(formatEta(-5)).toBe('Calculating...');
-    });
-
-    it('formats seconds', () => {
-        expect(formatEta(30)).toBe('30s');
-        expect(formatEta(1)).toBe('1s');
-    });
-
-    it('formats minutes and seconds', () => {
-        expect(formatEta(90)).toBe('1m 30s');
-        expect(formatEta(125)).toBe('2m 5s');
-    });
-
-    it('formats hours and minutes', () => {
-        expect(formatEta(3661)).toBe('1h 1m');
-        expect(formatEta(7200)).toBe('2h 0m');
-    });
-});
-
-describe('formatDuration', () => {
-    it('formats sub-second durations as milliseconds', () => {
-        expect(formatDuration(0.5)).toBe('500ms');
-        expect(formatDuration(0.001)).toBe('1ms');
-    });
-
-    it('formats seconds with one decimal', () => {
-        expect(formatDuration(5.3)).toBe('5.3s');
-        expect(formatDuration(30.0)).toBe('30.0s');
-    });
-
-    it('formats minutes and seconds', () => {
-        expect(formatDuration(90)).toBe('1m 30s');
-        expect(formatDuration(125)).toBe('2m 5s');
-    });
-});
-
-describe('showNotification', () => {
-    beforeEach(() => {
-        document.body.innerHTML = '';
-    });
-
-    afterEach(() => {
-        document.body.innerHTML = '';
-    });
-
-    it('creates a notification element in the DOM', () => {
-        showNotification('Test message', 'info');
-        const notification = document.querySelector('.fixed.top-4.right-4');
-        expect(notification).not.toBeNull();
-        expect(notification.textContent).toBe('Test message');
-    });
-
-    it('applies error styling for error type', () => {
-        showNotification('Error!', 'error');
-        const notification = document.querySelector('.fixed.top-4.right-4');
-        expect(notification.classList.contains('bg-red-500')).toBe(true);
-    });
-
-    it('applies success styling for success type', () => {
-        showNotification('Success!', 'success');
-        const notification = document.querySelector('.fixed.top-4.right-4');
-        expect(notification.classList.contains('bg-green-500')).toBe(true);
-    });
-
-    it('applies info styling by default', () => {
-        showNotification('Info');
-        const notification = document.querySelector('.fixed.top-4.right-4');
-        expect(notification.classList.contains('bg-nlr-blue')).toBe(true);
-    });
-});

From 3dc1705a5178815a9d361583d9e293398f9ef4e0 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 17:04:31 -0700
Subject: [PATCH 097/173] Refactor: Delete non react js modules

---
 app/static/js/app.js                     |  51 --
 app/static/js/modules/about.js           |  55 --
 app/static/js/modules/analysis.js        | 421 ----------
 app/static/js/modules/api.js             |  51 --
 app/static/js/modules/debounce.js        |  16 -
 app/static/js/modules/dom.js             |  73 --
 app/static/js/modules/file-browser.js    | 205 -----
 app/static/js/modules/folder-browser.js  | 952 -----------------------
 app/static/js/modules/formatters.js      |  60 --
 app/static/js/modules/icons.js           |  26 -
 app/static/js/modules/logs.js            | 425 ----------
 app/static/js/modules/notify.js          |  25 -
 app/static/js/modules/settings.js        | 402 ----------
 app/static/js/modules/sorting-helpers.js |  40 -
 app/static/js/modules/state.js           |  75 --
 app/static/js/modules/stepper.js         |  83 --
 app/static/js/modules/upload-control.js  |  54 --
 app/static/js/modules/upload-exec.js     | 226 ------
 app/static/js/modules/upload-init.js     |  53 --
 19 files changed, 3293 deletions(-)
 delete mode 100644 app/static/js/app.js
 delete mode 100644 app/static/js/modules/about.js
 delete mode 100644 app/static/js/modules/analysis.js
 delete mode 100644 app/static/js/modules/api.js
 delete mode 100644 app/static/js/modules/debounce.js
 delete mode 100644 app/static/js/modules/dom.js
 delete mode 100644 app/static/js/modules/file-browser.js
 delete mode 100644 app/static/js/modules/folder-browser.js
 delete mode 100644 app/static/js/modules/formatters.js
 delete mode 100644 app/static/js/modules/icons.js
 delete mode 100644 app/static/js/modules/logs.js
 delete mode 100644 app/static/js/modules/notify.js
 delete mode 100644 app/static/js/modules/settings.js
 delete mode 100644 app/static/js/modules/sorting-helpers.js
 delete mode 100644 app/static/js/modules/state.js
 delete mode 100644 app/static/js/modules/stepper.js
 delete mode 100644 app/static/js/modules/upload-control.js
 delete mode 100644 app/static/js/modules/upload-exec.js
 delete mode 100644 app/static/js/modules/upload-init.js

diff --git a/app/static/js/app.js b/app/static/js/app.js
deleted file mode 100644
index 08d325b..0000000
--- a/app/static/js/app.js
+++ /dev/null
@@ -1,51 +0,0 @@
-/**
- * modaq-upload - Entry Point
- *
- * Detects the current page via data-page attribute and dynamically
- * imports the appropriate module. Registers delegated click handlers
- * for data-action attributes (replacing inline onclick).
- */
-import {
-  closeAboutModal,
-  initAboutModal,
-  loadHeaderVersion,
-  openAboutModal,
-} from './modules/about.js';
-import { hideEl } from './modules/dom.js';
-import { goToStep } from './modules/stepper.js';
-
-// Global initialization (runs on every page)
-initAboutModal();
-loadHeaderVersion();
-
-// Delegated click handler for data-action attributes
-document.addEventListener('click', (e) => {
-  const target = /** @type {HTMLElement} */ (e.target).closest('[data-action]');
-  if (!target) return;
-
-  const action = /** @type {HTMLElement} */ (target).dataset.action;
-
-  if (action === 'open-about') {
-    openAboutModal();
-  } else if (action === 'close-about') {
-    closeAboutModal();
-  } else if (action === 'go-to-step') {
-    const step = Number(/** @type {HTMLElement} */ (target).dataset.step);
-    if (step) goToStep(step);
-  } else if (action === 'close-confirm-modal') {
-    hideEl('confirm-upload-modal');
-  }
-});
-
-// Page-specific module loading
-const page = document.body.dataset.page;
-
-if (page === 'upload') {
-  import('./modules/upload-init.js').then(({ initUpload }) => initUpload());
-} else if (page === 'files') {
-  import('./modules/file-browser.js').then(({ initFileBrowser }) => initFileBrowser());
-} else if (page === 'settings') {
-  import('./modules/settings.js').then(({ initSettings }) => initSettings());
-} else if (page === 'logs') {
-  import('./modules/logs.js').then(({ initLogs }) => initLogs());
-}
diff --git a/app/static/js/modules/about.js b/app/static/js/modules/about.js
deleted file mode 100644
index a206e82..0000000
--- a/app/static/js/modules/about.js
+++ /dev/null
@@ -1,55 +0,0 @@
-/**
- * About modal functionality.
- */
-import { apiGet } from './api.js';
-import { hideEl, setText, showEl } from './dom.js';
-import state from './state.js';
-
-/**
- * Load version info from the API and populate header badge.
- */
-export async function loadHeaderVersion() {
-  try {
-    const data = await apiGet('/api/settings/version');
-    state.appVersionData = data;
-    setText('header-version', data.version || '0.0.0');
-  } catch {
-    setText('header-version', '?');
-  }
-}
-
-export function openAboutModal() {
-  showEl('about-modal');
-  document.body.style.overflow = 'hidden';
-
-  if (state.appVersionData) {
-    setText('about-version', state.appVersionData.version || '0.0.0');
-    setText('about-commit', state.appVersionData.commit || '-');
-    setText('about-branch', state.appVersionData.branch || '-');
-  }
-}
-
-export function closeAboutModal() {
-  hideEl('about-modal');
-  document.body.style.overflow = '';
-}
-
-/**
- * Initialize about modal event listeners.
- */
-export function initAboutModal() {
-  document.addEventListener('keydown', (e) => {
-    if (e.key === 'Escape') {
-      closeAboutModal();
-    }
-  });
-
-  const modal = document.getElementById('about-modal');
-  if (modal) {
-    modal.addEventListener('click', (e) => {
-      if (e.target === modal) {
-        closeAboutModal();
-      }
-    });
-  }
-}
diff --git a/app/static/js/modules/analysis.js b/app/static/js/modules/analysis.js
deleted file mode 100644
index d13ce1e..0000000
--- a/app/static/js/modules/analysis.js
+++ /dev/null
@@ -1,421 +0,0 @@
-/**
- * File analysis/validation and combined upload progress (Step 3).
- *
- * Performance: Instead of creating one DOM row per file (20K+ rows),
- * we track status in a Map and only render active uploads (max ~4-8 rows).
- * Status counters are maintained via simple arithmetic, not DOM scans.
- */
-import { apiGet } from './api.js';
-import { hideEl, setText, showEl } from './dom.js';
-import { formatBytes } from './formatters.js';
-import { showNotification } from './notify.js';
-import state from './state.js';
-import { setUploadStep } from './stepper.js';
-import { showCompletionSummary, updateProgressUI } from './upload-exec.js';
-
-// Progress weighting: analysis is typically slower than upload
-const ANALYSIS_WEIGHT = 70;
-const UPLOAD_WEIGHT = 30;
-
-/**
- * Cache of last-known status per filename.
- * @type {Map<string, string>}
- */
-const fileRowStatusCache = new Map();
-
-/** Pending file updates to flush in the next animation frame. @type {Map<string, any>} */
-const pendingFileUpdates = new Map();
-
-/** Whether a requestAnimationFrame is already scheduled. */
-let rafScheduled = false;
-
-/** Pending overall progress data to flush. @type {any} */
-let pendingProgressData = null;
-
-/**
- * Status counters — maintained via transitions, never DOM-scanned.
- * @type {{ pending: number, analyzing: number, ready: number, uploading: number, completed: number, skipped: number, failed: number }}
- */
-const counts = {
-  pending: 0,
-  analyzing: 0,
-  ready: 0,
-  uploading: 0,
-  completed: 0,
-  skipped: 0,
-  failed: 0,
-};
-
-/**
- * Reset internal state (call when starting a new job or resetting).
- */
-export function resetAnalysisState() {
-  fileRowStatusCache.clear();
-  pendingFileUpdates.clear();
-  pendingProgressData = null;
-  rafScheduled = false;
-
-  counts.pending = 0;
-  counts.analyzing = 0;
-  counts.ready = 0;
-  counts.uploading = 0;
-  counts.completed = 0;
-  counts.skipped = 0;
-  counts.failed = 0;
-}
-
-/**
- * Initialize status counters for a new job.
- * @param {number} totalFiles
- */
-export function initStatusCounts(totalFiles) {
-  resetAnalysisState();
-  counts.pending = totalFiles;
-  updateCounterDisplay();
-}
-
-/**
- * Check for an active upload job and restore UI state.
- */
-export async function checkForActiveJob() {
-  try {
-    const data = await apiGet('/api/upload/active');
-    if (!data.job_id) return;
-
-    state.currentJobId = data.job_id;
-    const job = data.job;
-
-    if (job.status === 'analyzing' || job.status === 'uploading') {
-      setUploadStep(3);
-      hideEl('folder-browser-panel');
-      showEl('upload-section');
-
-      if (job.status === 'uploading') {
-        setText('upload-phase-label', 'Uploading files...');
-      }
-
-      connectCombinedProgressStream(state.currentJobId);
-    } else if (job.status === 'ready') {
-      setUploadStep(3);
-      hideEl('folder-browser-panel');
-      showEl('upload-section');
-      connectCombinedProgressStream(state.currentJobId);
-    } else if (
-      job.status === 'completed' ||
-      job.status === 'failed' ||
-      job.status === 'cancelled'
-    ) {
-      setUploadStep(4);
-      hideEl('folder-browser-panel');
-      showEl('completion-section');
-      showCompletionSummary(job);
-    }
-  } catch (error) {
-    console.log('No active job found:', /** @type {Error} */ (error).message);
-  }
-}
-
-/**
- * Connect to SSE stream for combined validation + upload progress.
- * @param {string | null} jobId
- */
-export function connectCombinedProgressStream(jobId) {
-  if (state.eventSource) {
-    state.eventSource.close();
-  }
-
-  resetAnalysisState();
-
-  state.eventSource = new EventSource(`/api/upload/progress/${jobId}`);
-
-  let analysisTotal = 0;
-  let analysisCompleted = 0;
-
-  state.eventSource.onmessage = (event) => {
-    const data = JSON.parse(event.data);
-
-    if (data.error) {
-      showNotification(data.error, 'error');
-      state.eventSource?.close();
-      return;
-    }
-
-    // Analysis progress: queue per-file update for next frame
-    if (data.type === 'analysis_progress') {
-      queueFileUpdate(data.file);
-
-      // Set total from the first event that carries it
-      if (data.total_files && analysisTotal === 0) {
-        analysisTotal = data.total_files;
-        counts.pending = analysisTotal;
-        setText('files-total', data.total_files);
-      }
-
-      // Only count terminal statuses for progress bar (not pending/analyzing)
-      if (data.file.status !== 'pending' && data.file.status !== 'analyzing') {
-        analysisCompleted++;
-      }
-
-      // Update progress bar for analysis phase
-      if (analysisTotal > 0) {
-        const percent = (analysisCompleted / analysisTotal) * ANALYSIS_WEIGHT;
-        setProgressBar(percent);
-      }
-    }
-
-    // Analysis complete: transition to upload phase
-    if (data.type === 'analysis_complete') {
-      setProgressBar(ANALYSIS_WEIGHT);
-      setPhaseLabel('Preparing upload...');
-
-      if (!data.auto_upload) {
-        state.eventSource?.close();
-        state.eventSource = null;
-      }
-    }
-
-    // Auto-upload starting
-    if (data.type === 'auto_upload_starting') {
-      setPhaseLabel('Uploading files...');
-    }
-
-    // Upload progress updates (job-level data without a type field)
-    if (!data.type && data.job_id && data.status) {
-      if (data.status === 'uploading') {
-        // Remap upload progress into the UPLOAD_WEIGHT portion of the bar
-        const adjusted = {
-          ...data,
-          progress_percent: ANALYSIS_WEIGHT + (data.progress_percent / 100) * UPLOAD_WEIGHT,
-        };
-        pendingProgressData = adjusted;
-
-        // Queue per-file row updates
-        if (data.files) {
-          for (const file of data.files) {
-            queueFileUpdate(file);
-          }
-        }
-        scheduleRaf();
-      } else if (['completed', 'failed', 'cancelled'].includes(data.status)) {
-        state.eventSource?.close();
-        state.eventSource = null;
-        showCompletionSummary(data);
-      }
-    }
-  };
-
-  state.eventSource.onerror = () => {
-    if (state.eventSource) {
-      state.eventSource.close();
-      state.eventSource = null;
-      showNotification('Connection to server lost', 'error');
-    }
-  };
-}
-
-/**
- * Set the overall progress bar value (CSS transition handles smoothing).
- * @param {number} percent
- */
-function setProgressBar(percent) {
-  const progressBar = /** @type {HTMLElement | null} */ (document.getElementById('progress-bar'));
-  if (progressBar) progressBar.style.width = `${percent}%`;
-  setText('progress-percent', percent.toFixed(1));
-}
-
-/**
- * Update the phase label with an opacity fade transition.
- * @param {string} text
- */
-function setPhaseLabel(text) {
-  const phaseLabel = document.getElementById('upload-phase-label');
-  if (!phaseLabel || phaseLabel.textContent === text) return;
-  phaseLabel.style.opacity = '0';
-  setTimeout(() => {
-    phaseLabel.textContent = text;
-    phaseLabel.style.opacity = '1';
-  }, 150);
-}
-
-/**
- * Queue a file update for the next animation frame.
- * @param {any} fileData
- */
-function queueFileUpdate(fileData) {
-  pendingFileUpdates.set(fileData.filename, fileData);
-  scheduleRaf();
-}
-
-/** Schedule a requestAnimationFrame if not already pending. */
-function scheduleRaf() {
-  if (!rafScheduled) {
-    rafScheduled = true;
-    requestAnimationFrame(flushUpdates);
-  }
-}
-
-/**
- * Flush all pending updates in a single animation frame.
- * Updates status counters and active upload rows — no per-file DOM scan.
- */
-function flushUpdates() {
-  rafScheduled = false;
-
-  // Process all pending file updates: track status transitions and active files
-  for (const [filename, fileData] of pendingFileUpdates) {
-    const oldStatus = fileRowStatusCache.get(filename) || 'pending';
-    const newStatus = fileData.is_duplicate ? 'skipped' : fileData.status;
-
-    if (oldStatus !== newStatus) {
-      // Decrement old counter
-      if (oldStatus in counts) counts[/** @type {keyof counts} */ (oldStatus)]--;
-      // Increment new counter
-      if (newStatus in counts) counts[/** @type {keyof counts} */ (newStatus)]++;
-
-      fileRowStatusCache.set(filename, newStatus);
-    }
-  }
-
-  // Update active upload rows (only currently uploading/analyzing files)
-  updateActiveRows();
-
-  pendingFileUpdates.clear();
-
-  // Update status counter display
-  updateCounterDisplay();
-
-  // Flush pending overall progress
-  if (pendingProgressData) {
-    updateProgressUI(pendingProgressData);
-    pendingProgressData = null;
-  }
-}
-
-/**
- * Update the active upload rows — only render files that are currently
- * uploading or analyzing (max ~4-8 rows instead of 20K).
- */
-function updateActiveRows() {
-  const container = document.getElementById('upload-active-list');
-  if (!container) return;
-
-  // Collect currently active files from pending updates
-  /** @type {any[]} */
-  const activeFiles = [];
-  for (const [, fileData] of pendingFileUpdates) {
-    if (fileData.status === 'uploading' || fileData.status === 'analyzing') {
-      activeFiles.push(fileData);
-    }
-  }
-
-  // Also keep rows that are still active but weren't in this update batch
-  const existingRows = container.querySelectorAll('[data-upload-file]');
-  for (const row of existingRows) {
-    const filename = /** @type {HTMLElement} */ (row).getAttribute('data-upload-file') || '';
-    const currentStatus = fileRowStatusCache.get(filename);
-    if (currentStatus === 'uploading' || currentStatus === 'analyzing') {
-      // Keep it if not being replaced by a pending update
-      if (!pendingFileUpdates.has(filename)) continue;
-    } else {
-      // Status changed to non-active — remove row
-      row.remove();
-    }
-  }
-
-  // Upsert active file rows
-  for (const fileData of activeFiles) {
-    const row = container.querySelector(`[data-upload-file="${CSS.escape(fileData.filename)}"]`);
-
-    if (row) {
-      // Existing row — micro-update for progress
-      if (fileData.status === 'uploading') {
-        const bar = /** @type {HTMLElement | null} */ (row.querySelector('[data-progress-bar]'));
-        if (bar) bar.style.width = `${fileData.progress_percent || 0}%`;
-        const label = row.querySelector('[data-progress-label]');
-        if (label) {
-          label.textContent =
-            fileData.progress_percent != null ? `${fileData.progress_percent.toFixed(0)}%` : '';
-        }
-      } else {
-        // Status changed (e.g., pending → analyzing) — rebuild
-        row.innerHTML = buildActiveRowHTML(fileData);
-      }
-    } else {
-      // New active row
-      const div = document.createElement('div');
-      div.className = 'px-6 py-3 flex items-center justify-between';
-      div.setAttribute('data-upload-file', fileData.filename);
-      div.innerHTML = buildActiveRowHTML(fileData);
-      container.appendChild(div);
-    }
-  }
-
-  // Remove rows for files that completed/failed/skipped (no longer active)
-  for (const row of container.querySelectorAll('[data-upload-file]')) {
-    const filename = /** @type {HTMLElement} */ (row).getAttribute('data-upload-file') || '';
-    const status = fileRowStatusCache.get(filename);
-    if (status !== 'uploading' && status !== 'analyzing') {
-      row.remove();
-    }
-  }
-}
-
-/**
- * Build HTML for an active file row.
- * @param {any} fileData
- * @returns {string}
- */
-function buildActiveRowHTML(fileData) {
-  let statusIcon = '';
-  let statusText = '';
-
-  if (fileData.status === 'uploading') {
-    statusIcon =
-      '<svg class="spinner h-5 w-5 text-nlr-blue" fill="none" viewBox="0 0 24 24"><circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle><path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path></svg>';
-    const pct = fileData.progress_percent != null ? `${fileData.progress_percent.toFixed(0)}%` : '';
-    statusText = `
-      <div class="flex items-center space-x-2">
-        <div class="w-20 bg-gray-200 rounded-full h-2">
-          <div data-progress-bar class="bg-nlr-blue h-2 rounded-full transition-[width] duration-300 ease-out" style="width: ${fileData.progress_percent || 0}%"></div>
-        </div>
-        <span data-progress-label class="text-xs text-gray-500 w-8">${pct}</span>
-      </div>`;
-  } else if (fileData.status === 'analyzing') {
-    statusIcon =
-      '<svg class="spinner h-5 w-5 text-blue-500" fill="none" viewBox="0 0 24 24"><circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle><path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path></svg>';
-    statusText = '<span class="text-xs text-blue-600">Validating</span>';
-  }
-
-  return `
-    <div class="flex items-center space-x-3">
-        ${statusIcon || '<div class="h-5 w-5"></div>'}
-        <span class="text-sm text-gray-900">${fileData.filename}</span>
-    </div>
-    <div class="flex items-center space-x-4">
-        ${fileData.file_size_formatted ? `<span class="text-sm text-gray-500">${fileData.file_size_formatted}</span>` : ''}
-        ${statusText}
-    </div>
-  `;
-}
-
-/**
- * Update the status counter display from the counts object.
- * O(1) — just setting text on 5 elements.
- */
-function updateCounterDisplay() {
-  const active = counts.analyzing + counts.uploading;
-  const queued = counts.pending + counts.ready;
-  setText('upload-count-active', String(active));
-  setText('upload-count-completed', String(counts.completed));
-  setText('upload-count-skipped', String(counts.skipped));
-  setText('upload-count-failed', String(counts.failed));
-  setText('upload-count-queued', String(queued));
-}
-
-/**
- * @param {any} fileData
- * @returns {string}
- */
-export function formatFileSize(fileData) {
-  return fileData.file_size_formatted || formatBytes(fileData.file_size || 0);
-}
diff --git a/app/static/js/modules/api.js b/app/static/js/modules/api.js
deleted file mode 100644
index ca68506..0000000
--- a/app/static/js/modules/api.js
+++ /dev/null
@@ -1,51 +0,0 @@
-/**
- * Shared fetch wrappers for JSON API calls.
- */
-
-/**
- * GET a JSON endpoint. Throws on non-ok responses.
- * @param {string} url
- * @returns {Promise<any>}
- */
-export async function apiGet(url) {
-  const response = await fetch(url);
-  const data = await response.json();
-  if (!response.ok) throw new Error(data.error || `Request failed (${response.status})`);
-  return data;
-}
-
-/**
- * POST to a JSON endpoint. Throws on non-ok responses.
- * @param {string} url
- * @param {any} [body] - If provided, sent as JSON with Content-Type header.
- * @returns {Promise<any>}
- */
-export async function apiPost(url, body) {
-  /** @type {RequestInit} */
-  const options = { method: 'POST' };
-  if (body !== undefined) {
-    options.headers = { 'Content-Type': 'application/json' };
-    options.body = JSON.stringify(body);
-  }
-  const response = await fetch(url, options);
-  const data = await response.json();
-  if (!response.ok) throw new Error(data.error || `Request failed (${response.status})`);
-  return data;
-}
-
-/**
- * PUT to a JSON endpoint. Throws on non-ok responses.
- * @param {string} url
- * @param {any} body
- * @returns {Promise<any>}
- */
-export async function apiPut(url, body) {
-  const response = await fetch(url, {
-    method: 'PUT',
-    headers: { 'Content-Type': 'application/json' },
-    body: JSON.stringify(body),
-  });
-  const data = await response.json();
-  if (!response.ok) throw new Error(data.error || `Request failed (${response.status})`);
-  return data;
-}
diff --git a/app/static/js/modules/debounce.js b/app/static/js/modules/debounce.js
deleted file mode 100644
index d7b0b72..0000000
--- a/app/static/js/modules/debounce.js
+++ /dev/null
@@ -1,16 +0,0 @@
-/**
- * Debounce utility.
- */
-
-/**
- * @param {(...args: any[]) => void} fn
- * @param {number} delay
- * @returns {(...args: any[]) => void}
- */
-export function debounce(fn, delay) {
-  let timeout = 0;
-  return (/** @type {any[]} */ ...args) => {
-    clearTimeout(timeout);
-    timeout = window.setTimeout(() => fn(...args), delay);
-  };
-}
diff --git a/app/static/js/modules/dom.js b/app/static/js/modules/dom.js
deleted file mode 100644
index 0af1309..0000000
--- a/app/static/js/modules/dom.js
+++ /dev/null
@@ -1,73 +0,0 @@
-/**
- * DOM manipulation helpers.
- */
-
-/**
- * Set the text content of an element by ID.
- * @param {string} id
- * @param {string | number} value
- */
-export function setText(id, value) {
-  const el = document.getElementById(id);
-  if (el) el.textContent = String(value);
-}
-
-/**
- * Remove the `hidden` class from an element by ID.
- * @param {string} id
- */
-export function showEl(id) {
-  document.getElementById(id)?.classList.remove('hidden');
-}
-
-/**
- * Add the `hidden` class to an element by ID.
- * @param {string} id
- */
-export function hideEl(id) {
-  document.getElementById(id)?.classList.add('hidden');
-}
-
-/**
- * Disable a button, swap its label, run a callback, then restore.
- * @param {HTMLButtonElement | null} btn
- * @param {string} loadingText
- * @param {() => Promise<void>} callback
- */
-/**
- * Toggle the `hidden` class on an element by ID.
- * @param {string} id
- * @param {boolean} show - When true, remove `hidden`; when false, add it.
- */
-export function toggleEl(id, show) {
-  document.getElementById(id)?.classList.toggle('hidden', !show);
-}
-
-/**
- * Append text to an element's textContent by ID.
- * @param {string} id
- * @param {string} value
- */
-export function appendText(id, value) {
-  const el = document.getElementById(id);
-  if (el) el.textContent += String(value);
-}
-
-/**
- * Disable a button, swap its label, run a callback, then restore.
- * @param {HTMLButtonElement | null} btn
- * @param {string} loadingText
- * @param {() => Promise<void>} callback
- */
-export async function withLoadingButton(btn, loadingText, callback) {
-  if (!btn) return;
-  const originalText = btn.textContent;
-  btn.disabled = true;
-  btn.textContent = loadingText;
-  try {
-    await callback();
-  } finally {
-    btn.disabled = false;
-    btn.textContent = originalText;
-  }
-}
diff --git a/app/static/js/modules/file-browser.js b/app/static/js/modules/file-browser.js
deleted file mode 100644
index cfc58ea..0000000
--- a/app/static/js/modules/file-browser.js
+++ /dev/null
@@ -1,205 +0,0 @@
-/**
- * S3 file browser page functionality.
- */
-import { apiGet } from './api.js';
-import { debounce } from './debounce.js';
-import { hideEl, setText, showEl } from './dom.js';
-import { formatBytes } from './formatters.js';
-import { fileIcon, folderIcon } from './icons.js';
-import { showNotification } from './notify.js';
-import state from './state.js';
-
-export function initFileBrowser() {
-  const refreshBtn = document.getElementById('refresh-btn');
-  const searchInput = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('search-input')
-  );
-  const retryBtn = document.getElementById('retry-btn');
-  const closeSearchBtn = document.getElementById('close-search-btn');
-
-  if (!refreshBtn) return;
-
-  refreshBtn.addEventListener('click', () => loadFiles(state.currentPrefix));
-  retryBtn?.addEventListener('click', () => loadFiles(state.currentPrefix));
-  closeSearchBtn?.addEventListener('click', hideSearchResults);
-
-  const debouncedSearch = debounce(() => {
-    const query = searchInput?.value.trim() || '';
-    if (query.length >= 2) {
-      searchFiles(query);
-    } else {
-      hideSearchResults();
-    }
-  }, 300);
-  searchInput?.addEventListener('input', debouncedSearch);
-
-  loadSettings().then(() => loadFiles(''));
-}
-
-async function loadSettings() {
-  try {
-    const settings = await apiGet('/api/settings');
-    setText('bucket-name', settings.s3_bucket || 'No bucket configured');
-  } catch (_error) {
-    setText('bucket-name', 'Error loading settings');
-  }
-}
-
-/**
- * @param {string} prefix
- */
-async function loadFiles(prefix) {
-  state.currentPrefix = prefix;
-
-  showEl('loading-state');
-  hideEl('error-state');
-  hideEl('empty-state');
-  hideEl('file-list');
-
-  try {
-    const data = await apiGet(`/api/files/list?prefix=${encodeURIComponent(prefix)}`);
-
-    if (!data.success) {
-      throw new Error(data.error || 'Failed to load files');
-    }
-
-    hideEl('loading-state');
-
-    updateBreadcrumb(data.breadcrumbs || []);
-
-    if (data.folders.length === 0 && data.files.length === 0) {
-      showEl('empty-state');
-      return;
-    }
-
-    displayFiles(data.folders, data.files);
-  } catch (error) {
-    hideEl('loading-state');
-    showEl('error-state');
-    setText('error-message', /** @type {Error} */ (error).message);
-  }
-}
-
-/**
- * @param {Array<{ name: string, prefix: string }>} breadcrumbs
- */
-function updateBreadcrumb(breadcrumbs) {
-  const nav = document.getElementById('breadcrumb');
-  if (!nav) return;
-
-  nav.innerHTML = `
-        <a href="#" data-prefix="" class="text-nlr-blue hover:underline">Root</a>
-        ${breadcrumbs
-          .map(
-            (b) => `
-            <span class="text-gray-400">/</span>
-            <a href="#" data-prefix="${b.prefix}" class="text-nlr-blue hover:underline">${b.name}</a>
-        `,
-          )
-          .join('')}
-    `;
-
-  for (const link of nav.querySelectorAll('a')) {
-    link.addEventListener('click', (e) => {
-      e.preventDefault();
-      loadFiles(/** @type {HTMLElement} */ (link).dataset.prefix || '');
-    });
-  }
-}
-
-/**
- * @param {Array<{ name: string, prefix: string }>} folders
- * @param {Array<{ name: string, key: string, size: number, last_modified?: string }>} files
- */
-function displayFiles(folders, files) {
-  const fileList = document.getElementById('file-list');
-  if (!fileList) return;
-
-  fileList.innerHTML = [
-    ...folders.map(
-      (folder) => `
-            <div class="file-item px-6 py-3 flex items-center cursor-pointer" data-prefix="${folder.prefix}">
-                ${folderIcon()}
-                <span class="text-sm font-medium text-gray-900">${folder.name}/</span>
-            </div>
-        `,
-    ),
-    ...files.map(
-      (file) => `
-            <div class="file-item px-6 py-3 flex items-center justify-between">
-                <div class="flex items-center">
-                    ${fileIcon()}
-                    <span class="text-sm text-gray-900">${file.name}</span>
-                </div>
-                <div class="flex items-center space-x-4 text-sm text-gray-500">
-                    <span>${formatBytes(file.size)}</span>
-                    <span>${file.last_modified ? new Date(file.last_modified).toLocaleString() : '-'}</span>
-                </div>
-            </div>
-        `,
-    ),
-  ].join('');
-
-  showEl('file-list');
-
-  for (const el of fileList.querySelectorAll('[data-prefix]')) {
-    el.addEventListener('click', () =>
-      loadFiles(/** @type {HTMLElement} */ (el).dataset.prefix || ''),
-    );
-  }
-}
-
-/**
- * @param {string} query
- */
-async function searchFiles(query) {
-  try {
-    const data = await apiGet(
-      `/api/files/search?query=${encodeURIComponent(query)}&prefix=${encodeURIComponent(state.currentPrefix)}`,
-    );
-    showSearchResults(data.files, query);
-  } catch (error) {
-    showNotification(/** @type {Error} */ (error).message, 'error');
-  }
-}
-
-/**
- * @param {Array<{ name: string, key: string, size: number }>} files
- * @param {string} _query
- */
-function showSearchResults(files, _query) {
-  const container = document.getElementById('search-results');
-  const list = document.getElementById('search-results-list');
-  if (!container || !list) return;
-
-  list.innerHTML =
-    files.length === 0
-      ? '<div class="px-6 py-4 text-center text-gray-500">No files found</div>'
-      : files
-          .map(
-            (file) => `
-                <div class="px-6 py-3 flex items-center justify-between">
-                    <div class="flex items-center">
-                        ${fileIcon()}
-                        <div>
-                            <div class="text-sm text-gray-900">${file.name}</div>
-                            <div class="text-xs text-gray-500">${file.key}</div>
-                        </div>
-                    </div>
-                    <span class="text-sm text-gray-500">${formatBytes(file.size)}</span>
-                </div>
-            `,
-          )
-          .join('');
-
-  showEl('search-results');
-}
-
-function hideSearchResults() {
-  hideEl('search-results');
-
-  const searchInput = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('search-input')
-  );
-  if (searchInput) searchInput.value = '';
-}
diff --git a/app/static/js/modules/folder-browser.js b/app/static/js/modules/folder-browser.js
deleted file mode 100644
index a9e7292..0000000
--- a/app/static/js/modules/folder-browser.js
+++ /dev/null
@@ -1,952 +0,0 @@
-import { connectCombinedProgressStream, initStatusCounts } from './analysis.js';
-import { apiGet, apiPost } from './api.js';
-import { hideEl, setText, showEl } from './dom.js';
-import { formatBytes, formatMtime } from './formatters.js';
-import { fileIcon, folderIcon } from './icons.js';
-import { showNotification } from './notify.js';
-import { toggleSort, updateSortIndicators } from './sorting-helpers.js';
-/**
- * Inline folder browser and scan results for folder-based upload.
- */
-import state from './state.js';
-import { setUploadStep, showUploadSteps } from './stepper.js';
-
-/**
- * Initialize the inline folder browser and auto-load initial folder.
- */
-export async function initFolderBrowser() {
-  const panel = document.getElementById('folder-browser-panel');
-  if (!panel) return;
-
-  document.getElementById('select-folder-btn')?.addEventListener('click', selectCurrentFolder);
-
-  // Delegated click handler for folder navigation (shared across 3 containers)
-  /** @param {Event} e */
-  function handleFolderNavClick(e) {
-    const target = /** @type {HTMLElement} */ (e.target).closest('[data-action="navigate-folder"]');
-    if (target) {
-      loadFolderBrowser(/** @type {HTMLElement} */ (target).dataset.path || '');
-    }
-  }
-
-  document.getElementById('folder-list')?.addEventListener('click', handleFolderNavClick);
-  document.getElementById('folder-quick-links')?.addEventListener('click', handleFolderNavClick);
-  document.getElementById('folder-breadcrumb')?.addEventListener('click', handleFolderNavClick);
-
-  // Click handler for Review table (folder expand/collapse)
-  const scanSection = document.getElementById('scan-results-section');
-  if (scanSection) {
-    scanSection.addEventListener('click', (e) => {
-      const folderHeader = /** @type {HTMLElement} */ (e.target).closest('[data-folder-header]');
-      if (folderHeader) {
-        toggleFolderExpand(/** @type {HTMLTableRowElement} */ (folderHeader));
-      }
-    });
-  }
-
-  // Sort header click handler (File browser table)
-  const fileTableHead = document.getElementById('file-table-head');
-  if (fileTableHead) {
-    fileTableHead.addEventListener('click', (e) => {
-      const th = /** @type {HTMLElement} */ (e.target).closest('[data-file-sort]');
-      if (th) {
-        sortBrowserFileTable(/** @type {HTMLElement} */ (th).dataset.fileSort || 'name');
-      }
-    });
-  }
-
-  // Auto-load: use last folder or default from settings
-  const lastFolder = localStorage.getItem('lastUploadFolder');
-  if (lastFolder) {
-    loadFolderBrowser(lastFolder);
-  } else {
-    try {
-      const settings = await apiGet('/api/settings');
-      loadFolderBrowser(settings.default_upload_folder || '');
-    } catch (_error) {
-      loadFolderBrowser('');
-    }
-  }
-}
-
-/**
- * Load folder contents from the backend.
- * Uses raw fetch for complex retry-on-failure logic.
- * @param {string} path
- * @param {boolean} [isRetry]
- */
-export async function loadFolderBrowser(path, isRetry = false) {
-  hideEl('folder-list');
-  hideEl('folder-error');
-  showEl('folder-loading');
-
-  try {
-    const url = path ? `/api/files/browse?path=${encodeURIComponent(path)}` : '/api/files/browse';
-    const response = await fetch(url);
-    const data = await response.json();
-
-    if (!response.ok) {
-      if (path && !isRetry) {
-        console.warn(`Failed to load saved folder "${path}", falling back to home`);
-        loadFolderBrowser('', true);
-        return;
-      }
-      throw new Error(data.error || 'Failed to load folder');
-    }
-
-    // Update quick links (using data-action instead of onclick)
-    const quickLinksContainer = document.getElementById('folder-quick-links');
-    if (quickLinksContainer) {
-      const lastUsedFolder = localStorage.getItem('lastUploadFolder');
-      let quickLinksHtml = '';
-
-      if (lastUsedFolder && lastUsedFolder !== data.current_path) {
-        const lastFolderName = lastUsedFolder.split('/').pop() || lastUsedFolder;
-        quickLinksHtml += `
-                    <button class="px-3 py-1 text-sm bg-nlr-blue text-white hover:bg-nlr-blue-light rounded-md whitespace-nowrap"
-                            data-action="navigate-folder" data-path="${lastUsedFolder}">
-                        Last: ${lastFolderName}
-                    </button>
-                `;
-      }
-
-      quickLinksHtml += data.quick_links
-        .map(
-          (/** @type {{ name: string, path: string }} */ link) => `
-                <button class="px-3 py-1 text-sm bg-gray-200 hover:bg-gray-300 rounded-md whitespace-nowrap"
-                        data-action="navigate-folder" data-path="${link.path}">
-                    ${link.name}
-                </button>
-            `,
-        )
-        .join('');
-
-      quickLinksContainer.innerHTML = quickLinksHtml;
-    }
-
-    // Update breadcrumbs
-    const breadcrumbContainer = document.getElementById('folder-breadcrumb');
-    if (breadcrumbContainer) {
-      breadcrumbContainer.innerHTML = data.breadcrumbs
-        .map(
-          (/** @type {{ name: string, path: string }} */ crumb, /** @type {number} */ i) => `
-                ${i > 0 ? '<span class="text-gray-400">/</span>' : ''}
-                <button class="text-nlr-blue hover:underline whitespace-nowrap"
-                        data-action="navigate-folder" data-path="${crumb.path}">
-                    ${crumb.name}
-                </button>
-            `,
-        )
-        .join('');
-    }
-
-    // Update MCAP count
-    setText('folder-mcap-count', data.mcap_count);
-
-    // Enable select button and store current path
-    const selectFolderBtn = /** @type {HTMLButtonElement | null} */ (
-      document.getElementById('select-folder-btn')
-    );
-    if (selectFolderBtn) {
-      selectFolderBtn.disabled = false;
-      selectFolderBtn.dataset.path = data.current_path;
-    }
-
-    // Update bottom summary with MCAP count
-    if (data.mcap_count > 0) {
-      setText(
-        'folder-select-summary',
-        `${data.mcap_count} MCAP file${data.mcap_count === 1 ? '' : 's'} in this folder.`,
-      );
-    } else {
-      setText(
-        'folder-select-summary',
-        'Navigate to the folder containing your MCAP files, then click Upload Folder.',
-      );
-    }
-
-    // Render folder list
-    hideEl('folder-loading');
-    showEl('folder-list');
-
-    const folderList = document.getElementById('folder-list');
-    if (folderList) {
-      if (data.folders.length === 0 && data.files.length === 0) {
-        folderList.innerHTML =
-          '<div class="p-8 text-center text-gray-500">This folder is empty</div>';
-      } else {
-        folderList.innerHTML = [
-          data.parent_path
-            ? `
-                        <div class="px-6 py-3 flex items-center cursor-pointer hover:bg-gray-50"
-                             data-action="navigate-folder" data-path="${data.parent_path}">
-                            <svg class="h-5 w-5 text-gray-400 mr-3" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                                <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M11 17l-5-5m0 0l5-5m-5 5h12" />
-                            </svg>
-                            <span class="text-sm text-gray-600">..</span>
-                        </div>
-                    `
-            : '',
-          ...data.folders.map(
-            (/** @type {{ name: string, path: string, mcap_count: number }} */ folder) => `
-                        <div class="px-6 py-3 flex items-center justify-between cursor-pointer hover:bg-gray-50"
-                             data-action="navigate-folder" data-path="${folder.path}"
-                             data-folder-name="${folder.name}">
-                            <div class="flex items-center">
-                                ${folderIcon()}
-                                <span class="text-sm font-medium text-gray-900">${folder.name}</span>
-                            </div>
-                            ${
-                              folder.mcap_count > 0
-                                ? `<span class="folder-mcap-badge text-xs text-gray-500" title="Direct files only, not including subfolders">${folder.mcap_count} mcap</span>`
-                                : '<span class="folder-mcap-badge text-xs text-gray-500"></span>'
-                            }
-                        </div>
-                    `,
-          ),
-        ].join('');
-      }
-    }
-
-    // Render MCAP file table
-    if (data.files.length > 0) {
-      state.browserFiles = data.files;
-      state.browserFileSortConfig = state.browserFileSortConfig || {
-        column: 'name',
-        ascending: true,
-      };
-      renderBrowserFileTable();
-      showEl('file-table-section');
-    } else {
-      state.browserFiles = [];
-      hideEl('file-table-section');
-    }
-
-    // Start background scan for upload status enrichment
-    startBrowserScan(data.current_path);
-  } catch (error) {
-    hideEl('folder-loading');
-    showEl('folder-error');
-    setText('folder-error-message', /** @type {Error} */ (error).message);
-  }
-}
-
-/**
- * Select the current folder and populate Step 2 from stored browser scan data.
- * The browser scan has already accumulated state.scanFileStatuses and state.scanFilePaths.
- */
-function selectCurrentFolder() {
-  const btn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('select-folder-btn')
-  );
-  if (!btn) return;
-
-  const folderPath = btn.dataset.path;
-  if (!folderPath) return;
-
-  state.selectedFolderPath = folderPath;
-  state.scanFolderPath = folderPath;
-  localStorage.setItem('lastUploadFolder', folderPath);
-
-  // Transition to Step 2 — populate from stored browser scan data
-  showUploadSteps(2);
-  state.reviewSortConfig = { column: 'filename', ascending: true };
-
-  setText('selected-folder-path', folderPath);
-  setText('scan-total', String(state.scanFileStatuses.length));
-  setText('scan-total-volume', formatBytes(state.scanTotalSize));
-  const uploadedCount = state.scanFileStatuses.filter(
-    (/** @type {any} */ f) => f.already_uploaded,
-  ).length;
-  setText('scan-already-uploaded', String(uploadedCount));
-
-  // Clear and populate review table from stored scan results
-  const tbody = document.getElementById('scan-file-list');
-  if (tbody) tbody.innerHTML = '';
-
-  for (let i = 0; i < state.browserScanResults.length; i++) {
-    appendFolderToReviewTable(state.browserScanResults[i], i);
-  }
-
-  // Hide scan progress (scan already done), enable continue button
-  hideEl('scan-progress-container');
-  const continueBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('continue-upload-btn')
-  );
-  if (continueBtn) {
-    continueBtn.disabled = state.scanFilePaths.length === 0;
-  }
-
-  const hideUploadedCheckbox = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('scan-hide-uploaded')
-  );
-  if (hideUploadedCheckbox) {
-    hideUploadedCheckbox.checked = false;
-    hideUploadedCheckbox.onchange = () => applyScanFileFilter();
-  }
-
-  const hideCompletedFoldersCheckbox = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('scan-hide-completed-folders')
-  );
-  if (hideCompletedFoldersCheckbox) {
-    hideCompletedFoldersCheckbox.checked = false;
-    hideCompletedFoldersCheckbox.onchange = () => applyScanFileFilter();
-  }
-
-  hideEl('folder-browser-panel');
-  showEl('scan-results-section');
-}
-
-/**
- * Green checkmark SVG for fully-uploaded folders.
- * @returns {string}
- */
-function checkmarkIcon() {
-  return '<svg class="h-4 w-4 text-green-500 inline-block ml-1" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7" /></svg>';
-}
-
-/**
- * Start a background cache-only scan for the current folder to enrich
- * folder rows with upload status. Called automatically after navigation.
- * @param {string} folderPath
- */
-async function startBrowserScan(folderPath) {
-  // Cancel any existing browser scan
-  if (state.browserScanJobId) {
-    try {
-      await apiPost(`/api/upload/cancel/${state.browserScanJobId}`);
-    } catch (_error) {
-      // Scan may have already finished
-    }
-  }
-  if (state.browserScanEventSource) {
-    state.browserScanEventSource.close();
-    state.browserScanEventSource = null;
-  }
-
-  // Reset browser scan state
-  state.browserScanResults = [];
-  state.browserScanJobId = null;
-  state.browserScanComplete = false;
-  state.scanFileStatuses = [];
-  state.scanFilePaths = [];
-  state.scanTotalSize = 0;
-
-  // Running aggregation map: immediate child folder name → { totalFiles, alreadyUploaded }
-  /** @type {Map<string, { totalFiles: number, alreadyUploaded: number }>} */
-  const folderAggregation = new Map();
-
-  // Root file aggregation (for files in the browsed folder itself)
-  let rootTotalFiles = 0;
-  let rootAlreadyUploaded = 0;
-
-  // Disable Upload button until scan completes
-  const selectBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('select-folder-btn')
-  );
-  if (selectBtn) {
-    selectBtn.disabled = true;
-    const btnSpan = selectBtn.querySelector('span');
-    if (btnSpan) btnSpan.textContent = 'Scanning...';
-  }
-
-  // Show scan status bar
-  showEl('browser-scan-status');
-  const spinner = document.getElementById('browser-scan-spinner');
-  if (spinner) spinner.classList.remove('hidden');
-  setText('browser-scan-text', 'Scanning folders...');
-
-  // Wire up hide-uploaded toggle
-  const hideCheckbox = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('browser-hide-uploaded')
-  );
-  if (hideCheckbox) {
-    hideCheckbox.onchange = () => applyBrowserHideUploaded(hideCheckbox.checked);
-  }
-
-  try {
-    const data = await apiPost('/api/upload/scan-folder-async', {
-      folder_path: folderPath,
-      cache_only: true,
-    });
-
-    state.browserScanJobId = data.job_id;
-
-    // Connect SSE for browser scan progress
-    state.browserScanEventSource = new EventSource(`/api/upload/progress/${data.job_id}`);
-
-    state.browserScanEventSource.onmessage = (event) => {
-      const eventData = JSON.parse(event.data);
-
-      if (eventData.error) {
-        showNotification(eventData.error, 'error');
-        closeBrowserScan();
-        enableUploadButton(folderPath);
-        return;
-      }
-
-      if (eventData.type === 'scan_started') {
-        setText('browser-scan-text', `Scanning 0 of ${eventData.folders_total} folders...`);
-      }
-
-      if (eventData.type === 'scan_folder_complete') {
-        const folder = eventData.folder;
-        const totals = eventData.running_totals;
-
-        // Store result
-        state.browserScanResults.push(folder);
-        state.scanTotalSize = totals.total_size;
-
-        // Accumulate file statuses and paths
-        for (const file of folder.files) {
-          state.scanFileStatuses.push(file);
-          if (!file.already_uploaded) {
-            state.scanFilePaths.push(file.path);
-          }
-        }
-
-        // Determine which immediate child this leaf folder belongs to
-        if (folder.relative_path === '.') {
-          // Root folder files
-          rootTotalFiles += folder.total_files;
-          rootAlreadyUploaded += folder.already_uploaded;
-          updateRootUploadStatus(rootTotalFiles, rootAlreadyUploaded);
-        } else {
-          // Extract the first path component
-          const firstSlash = folder.relative_path.indexOf('/');
-          const immediateChild =
-            firstSlash >= 0 ? folder.relative_path.substring(0, firstSlash) : folder.relative_path;
-
-          const existing = folderAggregation.get(immediateChild) || {
-            totalFiles: 0,
-            alreadyUploaded: 0,
-          };
-          existing.totalFiles += folder.total_files;
-          existing.alreadyUploaded += folder.already_uploaded;
-          folderAggregation.set(immediateChild, existing);
-
-          // Update the matching folder row in the browser
-          updateFolderRowBadge(immediateChild, existing);
-        }
-
-        // Update status bar
-        setText(
-          'browser-scan-text',
-          `Scanning ${eventData.folders_scanned} of ${eventData.folders_total} folders...`,
-        );
-
-        // Update Upload button summary
-        updateUploadButtonSummary();
-      }
-
-      if (eventData.type === 'scan_complete') {
-        closeBrowserScan();
-        state.browserScanComplete = true;
-
-        // Hide spinner, show final status
-        if (spinner) spinner.classList.add('hidden');
-
-        const totalFiles = state.scanFileStatuses.length;
-        const alreadyUploaded = state.scanFileStatuses.filter(
-          (/** @type {any} */ f) => f.already_uploaded,
-        ).length;
-        const toUpload = totalFiles - alreadyUploaded;
-
-        if (totalFiles === 0) {
-          setText('browser-scan-text', 'No MCAP files found in subfolders.');
-          enableUploadButton(folderPath);
-        } else if (toUpload === 0) {
-          setText('browser-scan-text', `All ${totalFiles} files already uploaded.`);
-          enableUploadButton(folderPath, true);
-        } else {
-          setText(
-            'browser-scan-text',
-            `Scan complete: ${toUpload} to upload, ${alreadyUploaded} already uploaded.`,
-          );
-          enableUploadButton(folderPath);
-        }
-      }
-    };
-
-    state.browserScanEventSource.onerror = () => {
-      closeBrowserScan();
-      enableUploadButton(folderPath);
-    };
-  } catch (error) {
-    showNotification(/** @type {Error} */ (error).message, 'error');
-    closeBrowserScan();
-    enableUploadButton(folderPath);
-  }
-}
-
-/**
- * Close the browser scan SSE connection.
- */
-function closeBrowserScan() {
-  if (state.browserScanEventSource) {
-    state.browserScanEventSource.close();
-    state.browserScanEventSource = null;
-  }
-}
-
-/**
- * Re-enable the Upload button after scan completes.
- * @param {string} folderPath
- * @param {boolean} [allUploaded] - If true, keep button disabled (nothing to upload)
- */
-function enableUploadButton(folderPath, allUploaded = false) {
-  const selectBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('select-folder-btn')
-  );
-  if (!selectBtn) return;
-
-  if (allUploaded) {
-    selectBtn.disabled = true;
-    const btnSpan = selectBtn.querySelector('span');
-    if (btnSpan) btnSpan.textContent = 'All Files Uploaded';
-  } else {
-    selectBtn.disabled = false;
-    selectBtn.dataset.path = folderPath;
-    updateUploadButtonSummary();
-  }
-}
-
-/**
- * Update the Upload button label and summary text based on scan data.
- */
-function updateUploadButtonSummary() {
-  const toUploadCount = state.scanFilePaths.length;
-  const totalCount = state.scanFileStatuses.length;
-  const uploadedCount = totalCount - toUploadCount;
-
-  const selectBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('select-folder-btn')
-  );
-  if (selectBtn) {
-    const btnSpan = selectBtn.querySelector('span');
-    if (btnSpan) {
-      if (toUploadCount > 0) {
-        btnSpan.textContent = `Upload ${toUploadCount} Files`;
-      } else if (totalCount > 0) {
-        btnSpan.textContent = 'All Files Uploaded';
-      } else {
-        btnSpan.textContent = 'Upload This Folder';
-      }
-    }
-  }
-
-  // Update bottom summary text
-  if (totalCount > 0) {
-    const sizeToUpload = state.scanFileStatuses
-      .filter((/** @type {any} */ f) => !f.already_uploaded)
-      .reduce((/** @type {number} */ sum, /** @type {any} */ f) => sum + f.size, 0);
-    if (toUploadCount > 0) {
-      setText(
-        'folder-select-summary',
-        `${toUploadCount} of ${totalCount} files to upload (${formatBytes(sizeToUpload)}). ${uploadedCount} already uploaded.`,
-      );
-    } else {
-      setText('folder-select-summary', `All ${totalCount} files are already uploaded.`);
-    }
-  }
-}
-
-/**
- * Update a folder row's badge with scan results.
- * @param {string} folderName
- * @param {{ totalFiles: number, alreadyUploaded: number }} stats
- */
-function updateFolderRowBadge(folderName, stats) {
-  const folderList = document.getElementById('folder-list');
-  if (!folderList) return;
-
-  const row = folderList.querySelector(`[data-folder-name="${CSS.escape(folderName)}"]`);
-  if (!row) return;
-
-  const badge = row.querySelector('.folder-mcap-badge');
-  if (!badge) return;
-
-  const allUploaded = stats.alreadyUploaded === stats.totalFiles && stats.totalFiles > 0;
-
-  if (allUploaded) {
-    badge.innerHTML = `${stats.totalFiles} mcap (${stats.alreadyUploaded} uploaded) ${checkmarkIcon()}`;
-    row.classList.add('bg-green-50');
-    /** @type {HTMLElement} */ (row).dataset.allUploaded = 'true';
-  } else if (stats.alreadyUploaded > 0) {
-    badge.textContent = `${stats.totalFiles} mcap (${stats.alreadyUploaded} uploaded)`;
-  } else {
-    badge.textContent = `${stats.totalFiles} mcap`;
-  }
-}
-
-/**
- * Update the root upload status in the MCAP count info bar.
- * @param {number} totalFiles
- * @param {number} alreadyUploaded
- */
-function updateRootUploadStatus(totalFiles, alreadyUploaded) {
-  const statusEl = document.getElementById('browser-root-upload-status');
-  if (!statusEl) return;
-
-  if (alreadyUploaded === totalFiles && totalFiles > 0) {
-    statusEl.innerHTML = `<span class="text-green-600">(${alreadyUploaded} uploaded) ${checkmarkIcon()}</span>`;
-  } else if (alreadyUploaded > 0) {
-    statusEl.innerHTML = `<span class="text-gray-600">(${alreadyUploaded} of ${totalFiles} uploaded)</span>`;
-  }
-}
-
-/**
- * Toggle visibility of fully-uploaded folder rows in the browser.
- * @param {boolean} hide
- */
-function applyBrowserHideUploaded(hide) {
-  const folderList = document.getElementById('folder-list');
-  if (!folderList) return;
-
-  const rows = folderList.querySelectorAll('[data-folder-name]');
-  for (const row of rows) {
-    if (hide && /** @type {HTMLElement} */ (row).dataset.allUploaded === 'true') {
-      /** @type {HTMLElement} */ (row).classList.add('hidden');
-    } else {
-      /** @type {HTMLElement} */ (row).classList.remove('hidden');
-    }
-  }
-}
-
-/**
- * Append a scanned folder as a collapsed summary row in the review table.
- * File rows are only rendered on-demand when the folder header is expanded.
- * @param {{ relative_path: string, files: any[], total_files: number, already_uploaded: number, all_uploaded: boolean, error: string | null }} folderData
- * @param {number} folderIndex - Index into state.browserScanResults
- */
-function appendFolderToReviewTable(folderData, folderIndex) {
-  const tbody = document.getElementById('scan-file-list');
-  if (!tbody) return;
-
-  const folderLabel = folderData.relative_path === '.' ? '(root)' : folderData.relative_path;
-  const toUpload = folderData.total_files - folderData.already_uploaded;
-
-  // Collapsed folder header only — no file rows (rendered on expand)
-  const headerHtml = `
-    <tr class="bg-gray-100 cursor-pointer hover:bg-gray-200 select-none ${folderData.all_uploaded ? 'folder-all-uploaded' : ''}"
-        data-folder-header
-        data-folder-idx="${folderIndex}"
-        data-all-uploaded="${folderData.all_uploaded}"
-        data-expanded="false">
-      <td colspan="5" class="px-4 py-2">
-        <div class="flex items-center justify-between">
-          <div class="flex items-center">
-            <svg class="folder-chevron h-4 w-4 text-gray-400 mr-2 transition-transform flex-shrink-0" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-              <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 5l7 7-7 7" />
-            </svg>
-            ${folderIcon('h-4 w-4 text-nlr-yellow mr-2')}
-            <span class="text-sm font-medium text-gray-700">${folderLabel}</span>
-            ${folderData.all_uploaded ? checkmarkIcon() : ''}
-          </div>
-          <div class="flex items-center space-x-3">
-            <span class="text-xs text-gray-600">${folderData.total_files} files</span>
-            ${toUpload > 0 ? `<span class="text-xs font-medium text-green-700">${toUpload} to upload</span>` : ''}
-            ${folderData.already_uploaded > 0 ? `<span class="text-xs text-gray-500">${folderData.already_uploaded} uploaded</span>` : ''}
-            ${folderData.error ? `<span class="text-xs text-red-600 bg-red-100 px-2 py-0.5 rounded-full">Error</span>` : ''}
-          </div>
-        </div>
-      </td>
-    </tr>
-  `;
-
-  tbody.insertAdjacentHTML('beforeend', headerHtml);
-  applyScanFileFilter();
-}
-
-/**
- * Toggle expand/collapse of a folder in the review table.
- * @param {HTMLTableRowElement} headerRow
- */
-function toggleFolderExpand(headerRow) {
-  const idx = Number.parseInt(headerRow.dataset.folderIdx || '0', 10);
-  const folderData = state.browserScanResults[idx];
-  if (!folderData) return;
-
-  const isExpanded = headerRow.dataset.expanded === 'true';
-  const chevron = headerRow.querySelector('.folder-chevron');
-
-  if (isExpanded) {
-    // Collapse: remove file rows after this header until next header
-    let next = headerRow.nextElementSibling;
-    while (next && !next.hasAttribute('data-folder-header')) {
-      const toRemove = next;
-      next = next.nextElementSibling;
-      toRemove.remove();
-    }
-    headerRow.dataset.expanded = 'false';
-    if (chevron) chevron.classList.remove('rotate-90');
-  } else {
-    // Expand: render file rows after this header using a DocumentFragment
-    const fragment = document.createDocumentFragment();
-    for (const file of folderData.files) {
-      const tr = document.createElement('tr');
-      tr.className = file.already_uploaded ? 'bg-yellow-50' : '';
-      tr.dataset.alreadyUploaded = String(file.already_uploaded);
-      const dirPath = getDirectoryPart(file.relative_path);
-      tr.innerHTML = `
-        <td class="pl-8 pr-4 py-3">
-          <span class="text-sm ${file.already_uploaded ? 'text-gray-500' : 'text-gray-900'} truncate block" title="${file.filename}">${file.filename}</span>
-        </td>
-        <td class="px-4 py-3">
-          <span class="text-sm text-gray-500 truncate block" title="${dirPath}">${dirPath || '.'}</span>
-        </td>
-        <td class="px-4 py-3 whitespace-nowrap text-sm text-gray-500">${formatMtime(file.mtime)}</td>
-        <td class="px-4 py-3 whitespace-nowrap text-sm text-gray-500">${formatBytes(file.size)}</td>
-        <td class="px-4 py-3 whitespace-nowrap">
-          <span class="px-2 py-1 text-xs rounded-full ${file.already_uploaded ? 'bg-yellow-100 text-yellow-800' : 'bg-green-100 text-green-800'}">
-            ${file.already_uploaded ? 'Uploaded' : 'To Upload'}
-          </span>
-        </td>
-      `;
-      fragment.appendChild(tr);
-    }
-    headerRow.after(fragment);
-    headerRow.dataset.expanded = 'true';
-    if (chevron) chevron.classList.add('rotate-90');
-  }
-}
-
-/**
- * Get the directory part of a relative path (everything before the filename).
- * @param {string} relativePath
- * @returns {string}
- */
-function getDirectoryPart(relativePath) {
-  const lastSlash = relativePath.lastIndexOf('/');
-  return lastSlash >= 0 ? relativePath.substring(0, lastSlash) : '';
-}
-
-function applyScanFileFilter() {
-  const hideUploadedEl = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('scan-hide-uploaded')
-  );
-  const hideUploaded = hideUploadedEl?.checked || false;
-
-  const hideCompletedFoldersEl = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('scan-hide-completed-folders')
-  );
-  const hideCompletedFolders = hideCompletedFoldersEl?.checked || false;
-
-  const tbody = document.getElementById('scan-file-list');
-  if (!tbody) return;
-
-  // Determine which folder headers are for completed folders
-  /** @type {Set<Element>} */
-  const hiddenFolderHeaders = new Set();
-
-  // First pass: process folder headers
-  const folderHeaders = tbody.querySelectorAll('[data-folder-header]');
-  for (const header of folderHeaders) {
-    if (
-      hideCompletedFolders &&
-      /** @type {HTMLElement} */ (header).dataset.allUploaded === 'true'
-    ) {
-      header.classList.add('hidden');
-      hiddenFolderHeaders.add(header);
-    } else {
-      header.classList.remove('hidden');
-    }
-  }
-
-  // Second pass: process file rows
-  // For each file row, find its parent folder header (the nearest preceding [data-folder-header])
-  const allRows = /** @type {NodeListOf<HTMLElement>} */ (tbody.querySelectorAll('tr'));
-  /** @type {Element | null} */
-  let currentFolderHeader = null;
-
-  for (const row of allRows) {
-    if (row.hasAttribute('data-folder-header')) {
-      currentFolderHeader = row;
-      continue;
-    }
-
-    // This is a file row
-    const isUploaded = row.dataset.alreadyUploaded === 'true';
-    const inHiddenFolder = currentFolderHeader && hiddenFolderHeaders.has(currentFolderHeader);
-
-    if (inHiddenFolder || (hideUploaded && isUploaded)) {
-      row.classList.add('hidden');
-    } else {
-      row.classList.remove('hidden');
-    }
-  }
-}
-
-/**
- * Show the confirm upload modal.
- */
-export function showConfirmModal() {
-  if (!state.scanFileStatuses || state.scanFileStatuses.length === 0) {
-    showNotification('No files to upload', 'error');
-    return;
-  }
-
-  // Calculate size of non-uploaded files (default view)
-  updateConfirmModalCounts(false);
-
-  // Wire up force-reupload checkbox to update counts dynamically
-  const checkbox = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('force-reupload-checkbox')
-  );
-  if (checkbox) {
-    checkbox.checked = false;
-    checkbox.onchange = () => updateConfirmModalCounts(checkbox.checked);
-  }
-
-  showEl('confirm-skip-note');
-  showEl('confirm-upload-modal');
-}
-
-/**
- * Update confirm modal file count/size based on force-reupload state.
- * @param {boolean} forceReupload
- */
-function updateConfirmModalCounts(forceReupload) {
-  let uploadSize = 0;
-  let uploadCount = 0;
-  for (const file of state.scanFileStatuses) {
-    if (forceReupload || !file.already_uploaded) {
-      uploadSize += file.size;
-      uploadCount++;
-    }
-  }
-
-  setText('confirm-file-count', uploadCount);
-  setText('confirm-total-size', formatBytes(uploadSize));
-
-  if (forceReupload) {
-    hideEl('confirm-skip-note');
-  } else {
-    showEl('confirm-skip-note');
-  }
-}
-
-/**
- * Start the combined validate + upload flow.
- */
-export async function startCombinedUpload() {
-  // Close confirm modal
-  hideEl('confirm-upload-modal');
-
-  // Check force-reupload state
-  const forceCheckbox = /** @type {HTMLInputElement | null} */ (
-    document.getElementById('force-reupload-checkbox')
-  );
-  const forceReupload = forceCheckbox?.checked || false;
-
-  // Determine which file paths to send
-  const filePaths = forceReupload
-    ? state.scanFileStatuses.map((/** @type {any} */ f) => f.path)
-    : state.scanFilePaths;
-
-  if (!filePaths || filePaths.length === 0) {
-    showNotification('No files to upload', 'error');
-    return;
-  }
-
-  setUploadStep(3);
-
-  hideEl('scan-results-section');
-  showEl('upload-section');
-
-  // Set phase label
-  setText('upload-phase-label', 'Validating files...');
-
-  // Initialize file list with pending status
-  initUploadFileList(filePaths);
-
-  try {
-    /** @type {Record<string, any>} */
-    const requestBody = {
-      file_paths: filePaths,
-      auto_upload: true,
-    };
-    if (forceReupload) {
-      requestBody.skip_duplicates = false;
-    }
-
-    const data = await apiPost('/api/upload/bulk-analyze', requestBody);
-
-    state.currentJobId = data.job_id;
-    setText('files-total', data.total_files);
-
-    connectCombinedProgressStream(data.job_id);
-  } catch (error) {
-    showNotification(/** @type {Error} */ (error).message, 'error');
-  }
-}
-
-/**
- * Render the sortable file table in the folder browser.
- */
-function renderBrowserFileTable() {
-  const tbody = document.getElementById('file-table-body');
-  if (!tbody || !state.browserFiles) return;
-
-  const { column, ascending } = state.browserFileSortConfig;
-
-  const sorted = [...state.browserFiles].sort((a, b) => {
-    let cmp = 0;
-    if (column === 'name') {
-      cmp = a.name.localeCompare(b.name);
-    } else if (column === 'mtime') {
-      cmp = (a.mtime || 0) - (b.mtime || 0);
-    } else if (column === 'size') {
-      cmp = a.size - b.size;
-    }
-    return ascending ? cmp : -cmp;
-  });
-
-  tbody.innerHTML = sorted
-    .map(
-      (/** @type {{ name: string, size: number, mtime: number }} */ file) => `
-          <tr class="hover:bg-gray-50">
-            <td class="px-6 py-2">
-              <div class="flex items-center">
-                ${fileIcon('h-4 w-4 text-gray-400 mr-2 flex-shrink-0')}
-                <span class="text-sm text-gray-600 truncate">${file.name}</span>
-              </div>
-            </td>
-            <td class="px-4 py-2 text-sm text-gray-500 whitespace-nowrap">${formatMtime(file.mtime)}</td>
-            <td class="px-4 py-2 text-sm text-gray-500 text-right whitespace-nowrap">${formatBytes(file.size)}</td>
-          </tr>
-        `,
-    )
-    .join('');
-
-  // Update sort indicators
-  updateSortIndicators('[data-file-sort]', '.file-sort-indicator', 'fileSort', column, ascending);
-}
-
-/**
- * Sort the browser file table by column.
- * @param {string} column
- */
-function sortBrowserFileTable(column) {
-  if (!state.browserFileSortConfig) {
-    state.browserFileSortConfig = { column, ascending: true };
-  } else {
-    toggleSort(state.browserFileSortConfig, column);
-  }
-  renderBrowserFileTable();
-}
-
-/**
- * Initialize the upload view for a new job.
- * Instead of creating 20K+ DOM rows, initialize status counters and
- * clear the active upload area. Active files render on-demand.
- * @param {string[]} filePaths
- */
-function initUploadFileList(filePaths) {
-  const activeList = document.getElementById('upload-active-list');
-  if (activeList) activeList.innerHTML = '';
-
-  // Initialize counters (all files start as "pending")
-  initStatusCounts(filePaths.length);
-  setText('files-total', String(filePaths.length));
-}
diff --git a/app/static/js/modules/formatters.js b/app/static/js/modules/formatters.js
deleted file mode 100644
index d3ceaa8..0000000
--- a/app/static/js/modules/formatters.js
+++ /dev/null
@@ -1,60 +0,0 @@
-/**
- * Pure formatting functions for bytes, time, and dates.
- */
-
-/**
- * @param {number} bytes
- * @returns {string}
- */
-export function formatBytes(bytes) {
-  if (bytes === 0) return '0 B';
-  const k = 1024;
-  const sizes = ['B', 'KB', 'MB', 'GB', 'TB'];
-  const i = Math.floor(Math.log(bytes) / Math.log(k));
-  return `${Number.parseFloat((bytes / k ** i).toFixed(1))} ${sizes[i]}`;
-}
-
-/**
- * @param {number | null | undefined} seconds
- * @returns {string}
- */
-export function formatEta(seconds) {
-  if (!seconds || seconds < 0) return 'Calculating...';
-  if (seconds < 60) return `${seconds}s`;
-  if (seconds < 3600) return `${Math.floor(seconds / 60)}m ${seconds % 60}s`;
-  const hours = Math.floor(seconds / 3600);
-  const mins = Math.floor((seconds % 3600) / 60);
-  return `${hours}h ${mins}m`;
-}
-
-/**
- * @param {number} seconds
- * @returns {string}
- */
-export function formatDuration(seconds) {
-  if (seconds < 1) {
-    return `${Math.round(seconds * 1000)}ms`;
-  }
-  if (seconds < 60) {
-    return `${seconds.toFixed(1)}s`;
-  }
-  const mins = Math.floor(seconds / 60);
-  const secs = Math.round(seconds % 60);
-  return `${mins}m ${secs}s`;
-}
-
-/**
- * Format a Unix epoch (seconds) into a locale date string.
- * @param {number | null | undefined} epochSeconds
- * @returns {string}
- */
-export function formatMtime(epochSeconds) {
-  if (!epochSeconds) return '-';
-  return new Date(epochSeconds * 1000).toLocaleString('en-US', {
-    month: 'short',
-    day: 'numeric',
-    year: 'numeric',
-    hour: '2-digit',
-    minute: '2-digit',
-  });
-}
diff --git a/app/static/js/modules/icons.js b/app/static/js/modules/icons.js
deleted file mode 100644
index d9bc569..0000000
--- a/app/static/js/modules/icons.js
+++ /dev/null
@@ -1,26 +0,0 @@
-/**
- * Reusable SVG icon templates.
- */
-
-const FILE_ICON_PATH =
-  'M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z';
-
-const FOLDER_ICON_PATH = 'M2 6a2 2 0 012-2h5l2 2h5a2 2 0 012 2v6a2 2 0 01-2 2H4a2 2 0 01-2-2V6z';
-
-/**
- * File document SVG icon.
- * @param {string} [cls] - CSS classes (default: 'h-5 w-5 text-gray-400 mr-3')
- * @returns {string}
- */
-export function fileIcon(cls = 'h-5 w-5 text-gray-400 mr-3') {
-  return `<svg class="${cls}" fill="none" viewBox="0 0 24 24" stroke="currentColor"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="${FILE_ICON_PATH}" /></svg>`;
-}
-
-/**
- * Folder SVG icon.
- * @param {string} [cls] - CSS classes (default: 'h-5 w-5 text-nlr-yellow mr-3')
- * @returns {string}
- */
-export function folderIcon(cls = 'h-5 w-5 text-nlr-yellow mr-3') {
-  return `<svg class="${cls}" fill="currentColor" viewBox="0 0 20 20"><path d="${FOLDER_ICON_PATH}" /></svg>`;
-}
diff --git a/app/static/js/modules/logs.js b/app/static/js/modules/logs.js
deleted file mode 100644
index 1a65cfc..0000000
--- a/app/static/js/modules/logs.js
+++ /dev/null
@@ -1,425 +0,0 @@
-/**
- * Logs viewer page module.
- *
- * Loads log entries from /api/logs/entries with filtering, pagination,
- * expandable detail rows, and S3 sync trigger.
- */
-import { apiGet, apiPost } from './api.js';
-import { debounce } from './debounce.js';
-import { hideEl, setText, toggleEl, withLoadingButton } from './dom.js';
-import { showNotification } from './notify.js';
-import state from './state.js';
-
-/**
- * Format an ISO timestamp for display.
- * @param {string} iso
- * @returns {string}
- */
-function formatTimestamp(iso) {
-  try {
-    const d = new Date(iso);
-    return d.toLocaleString(undefined, {
-      year: 'numeric',
-      month: '2-digit',
-      day: '2-digit',
-      hour: '2-digit',
-      minute: '2-digit',
-      second: '2-digit',
-    });
-  } catch {
-    return iso;
-  }
-}
-
-/**
- * Return Tailwind classes for a log level badge.
- * @param {string} level
- * @returns {string}
- */
-function levelBadgeClass(level) {
-  const upper = level.toUpperCase();
-  if (upper === 'ERROR') return 'bg-red-100 text-red-800';
-  if (upper === 'WARNING') return 'bg-yellow-100 text-yellow-800';
-  return 'bg-blue-100 text-blue-800';
-}
-
-/**
- * Get the filter DOM elements (shared by clearFilters and applyFilters).
- */
-function getFilterEls() {
-  return {
-    date: /** @type {HTMLInputElement | null} */ (document.getElementById('filter-date')),
-    level: /** @type {HTMLSelectElement | null} */ (document.getElementById('filter-level')),
-    category: /** @type {HTMLSelectElement | null} */ (document.getElementById('filter-category')),
-    search: /** @type {HTMLInputElement | null} */ (document.getElementById('filter-search')),
-  };
-}
-
-/**
- * Render the log table body from an array of entries.
- * @param {Array<Record<string, unknown>>} entries
- */
-function renderLogTable(entries) {
-  const tbody = document.getElementById('log-table-body');
-  if (!tbody) return;
-
-  if (entries.length === 0) {
-    tbody.innerHTML =
-      '<tr><td colspan="5" class="px-4 py-8 text-center text-gray-500">No log entries found</td></tr>';
-    return;
-  }
-
-  let html = '';
-  for (const entry of entries) {
-    const ts = formatTimestamp(/** @type {string} */ (entry.timestamp) || '');
-    const level = /** @type {string} */ (entry.level) || 'INFO';
-    const category = /** @type {string} */ (entry.category) || '';
-    const event = /** @type {string} */ (entry.event) || '';
-    const message = /** @type {string} */ (entry.message) || '';
-    const metadata = /** @type {Record<string, unknown> | undefined} */ (entry.metadata);
-    const hasMetadata = metadata && Object.keys(metadata).length > 0;
-
-    const rowClass = hasMetadata ? 'cursor-pointer hover:bg-gray-50' : '';
-    const toggleAttr = hasMetadata ? 'data-log-toggle' : '';
-
-    html += `<tr class="${rowClass}" ${toggleAttr}>
-      <td class="px-4 py-2 text-xs text-gray-600 font-mono whitespace-nowrap">${ts}</td>
-      <td class="px-4 py-2"><span class="px-2 py-0.5 text-xs font-semibold rounded ${levelBadgeClass(level)}">${level}</span></td>
-      <td class="px-4 py-2"><span class="px-2 py-0.5 text-xs rounded bg-gray-100 text-gray-700">${category}</span></td>
-      <td class="px-4 py-2 text-xs text-gray-700 font-mono">${event}</td>
-      <td class="px-4 py-2 text-sm text-gray-800 truncate max-w-xs" title="${message.replace(/"/g, '&quot;')}">${message}</td>
-    </tr>`;
-
-    if (hasMetadata) {
-      const metaRows = Object.entries(metadata)
-        .map(
-          ([k, v]) =>
-            `<tr><td class="pr-4 text-gray-500 font-mono text-right align-top">${k}</td><td class="text-gray-800 break-all">${typeof v === 'object' ? JSON.stringify(v) : String(v)}</td></tr>`,
-        )
-        .join('');
-
-      html += `<tr class="hidden log-detail-row">
-        <td colspan="5" class="px-4 py-3 bg-gray-50">
-          <table class="text-xs"><tbody>${metaRows}</tbody></table>
-        </td>
-      </tr>`;
-    }
-  }
-
-  tbody.innerHTML = html;
-
-  // Wire toggle for expandable rows
-  for (const row of tbody.querySelectorAll('[data-log-toggle]')) {
-    row.addEventListener('click', () => {
-      const detail = row.nextElementSibling;
-      if (detail?.classList.contains('log-detail-row')) {
-        detail.classList.toggle('hidden');
-      }
-    });
-  }
-}
-
-/** Fetch and render log entries using current filters + pagination. */
-export async function loadLogEntries() {
-  const params = new URLSearchParams();
-  const { logFilters, logPagination } = state;
-
-  if (logFilters.date) params.set('date', logFilters.date);
-  if (logFilters.level) params.set('level', logFilters.level);
-  if (logFilters.category) params.set('category', logFilters.category);
-  if (logFilters.search) params.set('search', logFilters.search);
-  params.set('offset', String(logPagination.offset));
-  params.set('limit', String(logPagination.limit));
-
-  try {
-    const data = await apiGet(`/api/logs/entries?${params}`);
-
-    renderLogTable(data.entries || []);
-
-    // Update count label
-    const total = data.total || 0;
-    const from = total > 0 ? data.offset + 1 : 0;
-    const to = Math.min(data.offset + data.limit, total);
-    setText('log-count-label', `Showing ${from}-${to} of ${total}`);
-
-    // Pagination buttons
-    const prevBtn = /** @type {HTMLButtonElement | null} */ (
-      document.getElementById('prev-page-btn')
-    );
-    const nextBtn = /** @type {HTMLButtonElement | null} */ (
-      document.getElementById('next-page-btn')
-    );
-    if (prevBtn) prevBtn.disabled = data.offset <= 0;
-    if (nextBtn) nextBtn.disabled = data.offset + data.limit >= total;
-  } catch {
-    setText('log-count-label', 'Failed to load log entries');
-  }
-}
-
-/** Fetch and render log stats into the stat cards. */
-export async function loadLogStats() {
-  try {
-    const data = await apiGet('/api/logs/stats');
-
-    setText('stat-total', data.total_entries ?? 0);
-    setText('stat-today', data.today_entries ?? 0);
-    setText('stat-errors', data.level_counts?.ERROR ?? 0);
-    setText('stat-files', data.file_count ?? 0);
-  } catch {
-    // Silently fail — stats are non-critical
-  }
-}
-
-/** POST /api/logs/sync and show notification. */
-export async function syncLogs() {
-  const btn = /** @type {HTMLButtonElement | null} */ (document.getElementById('sync-logs-btn'));
-
-  await withLoadingButton(btn, 'Syncing...', async () => {
-    try {
-      const data = await apiPost('/api/logs/sync');
-
-      if (data.success) {
-        showNotification(`Synced ${data.synced} log files to S3`, 'success');
-      } else {
-        showNotification(`Sync failed: ${data.error || 'Unknown error'}`, 'error');
-      }
-    } catch (err) {
-      showNotification(`Sync error: ${err}`, 'error');
-    }
-  });
-}
-
-/** Track which CSV is currently previewed (to toggle on re-click). */
-let currentPreviewPath = '';
-
-/**
- * Extract time (HH:MM:SS) from a CSV filename like upload-summary-143022-abcd1234.csv.
- * @param {string} filename
- * @returns {string}
- */
-function extractTimeFromFilename(filename) {
-  const match = filename.match(/upload-summary-(\d{2})(\d{2})(\d{2})/);
-  if (match) return `${match[1]}:${match[2]}:${match[3]}`;
-  return '-';
-}
-
-/** Fetch CSV file list and render the Upload Summaries table. */
-export async function loadCsvFiles() {
-  try {
-    const data = await apiGet('/api/logs/files');
-    /** @type {Array<{date: string|null, filename: string, relative_path: string, size_bytes: number, type: string}>} */
-    const csvFiles = (data.files || []).filter(
-      (/** @type {{type: string}} */ f) => f.type === 'csv',
-    );
-
-    // Update badge
-    setText('csv-count-badge', csvFiles.length);
-    toggleEl('csv-count-badge', csvFiles.length > 0);
-
-    const tbody = document.getElementById('csv-table-body');
-    if (!tbody) return;
-
-    if (csvFiles.length === 0) {
-      tbody.innerHTML =
-        '<tr><td colspan="4" class="px-4 py-6 text-center text-gray-500 text-sm">No upload summaries found</td></tr>';
-      return;
-    }
-
-    let html = '';
-    for (const file of csvFiles) {
-      const date = file.date || '-';
-      const time = extractTimeFromFilename(file.filename);
-      const escapedPath = file.relative_path.replace(/"/g, '&quot;');
-
-      html += `<tr>
-        <td class="px-4 py-3 text-sm text-gray-700">${date}</td>
-        <td class="px-4 py-3 text-sm text-gray-700 font-mono">${time}</td>
-        <td class="px-4 py-3 text-sm text-gray-900 truncate" title="${file.filename}">${file.filename}</td>
-        <td class="px-4 py-3 text-right whitespace-nowrap">
-          <button class="csv-download-btn text-sm text-nlr-blue hover:underline mr-3" data-path="${escapedPath}">Download</button>
-          <button class="csv-view-btn text-sm text-nlr-blue hover:underline" data-path="${escapedPath}">View</button>
-        </td>
-      </tr>`;
-    }
-    tbody.innerHTML = html;
-
-    // Wire download buttons
-    for (const btn of tbody.querySelectorAll('.csv-download-btn')) {
-      btn.addEventListener('click', () => {
-        const path = /** @type {HTMLElement} */ (btn).dataset.path || '';
-        downloadCsv(path);
-      });
-    }
-
-    // Wire view buttons
-    for (const btn of tbody.querySelectorAll('.csv-view-btn')) {
-      btn.addEventListener('click', () => {
-        const path = /** @type {HTMLElement} */ (btn).dataset.path || '';
-        previewCsv(path);
-      });
-    }
-  } catch {
-    // Non-critical — silently fail
-  }
-}
-
-/**
- * Trigger a browser download for a CSV file.
- * @param {string} path - Relative path within the log directory
- */
-function downloadCsv(path) {
-  window.location.href = `/api/logs/csv-download?path=${encodeURIComponent(path)}`;
-}
-
-/**
- * Fetch and render a CSV preview inline. Toggle on re-click.
- * @param {string} path - Relative path within the log directory
- */
-async function previewCsv(path) {
-  const panel = document.getElementById('csv-preview-panel');
-  const content = document.getElementById('csv-preview-content');
-  if (!panel || !content) return;
-
-  // Toggle off if clicking the same file
-  if (currentPreviewPath === path && !panel.classList.contains('hidden')) {
-    hideEl('csv-preview-panel');
-    currentPreviewPath = '';
-    return;
-  }
-
-  currentPreviewPath = path;
-  content.innerHTML = '<p class="text-sm text-gray-500">Loading...</p>';
-  panel.classList.remove('hidden');
-
-  const filename = path.split('/').pop() || path;
-  setText('csv-preview-title', `Preview: ${filename}`);
-
-  try {
-    const data = await apiGet(`/api/logs/csv-preview?path=${encodeURIComponent(path)}`);
-
-    if (data.error) {
-      content.innerHTML = `<p class="text-sm text-red-600">${data.error}</p>`;
-      return;
-    }
-
-    const columns = /** @type {string[]} */ (data.columns || []);
-    const rows = /** @type {Array<Record<string, string>>} */ (data.rows || []);
-
-    if (columns.length === 0) {
-      content.innerHTML = '<p class="text-sm text-gray-500">Empty CSV</p>';
-      return;
-    }
-
-    let tableHtml = '<table class="w-full text-xs divide-y divide-gray-200">';
-    tableHtml += '<thead class="bg-gray-50"><tr>';
-    for (const col of columns) {
-      tableHtml += `<th class="px-3 py-2 text-left font-medium text-gray-500 uppercase">${col}</th>`;
-    }
-    tableHtml += '</tr></thead><tbody class="divide-y divide-gray-200">';
-    for (const row of rows) {
-      tableHtml += '<tr>';
-      for (const col of columns) {
-        const val = row[col] ?? '';
-        tableHtml += `<td class="px-3 py-2 text-gray-700 whitespace-nowrap">${val}</td>`;
-      }
-      tableHtml += '</tr>';
-    }
-    tableHtml += '</tbody></table>';
-    content.innerHTML = tableHtml;
-  } catch {
-    content.innerHTML = '<p class="text-sm text-red-600">Failed to load CSV preview</p>';
-  }
-}
-
-/** Reset all filters and reload. */
-export function clearFilters() {
-  state.logFilters = { date: null, level: null, category: null, search: '' };
-  state.logPagination = { offset: 0, limit: 100 };
-
-  const { date, level, category, search } = getFilterEls();
-  if (date) date.value = '';
-  if (level) level.value = '';
-  if (category) category.value = '';
-  if (search) search.value = '';
-
-  loadLogEntries();
-  loadLogStats();
-}
-
-/** Read current filter values from the DOM into state and reload. */
-function applyFilters() {
-  const { date, level, category, search } = getFilterEls();
-
-  state.logFilters.date = date?.value || null;
-  state.logFilters.level = level?.value || null;
-  state.logFilters.category = category?.value || null;
-  state.logFilters.search = search?.value || '';
-  state.logPagination.offset = 0;
-
-  loadLogEntries();
-}
-
-/** Initialize the logs page: load data and wire event handlers. */
-export function initLogs() {
-  // Reset state
-  state.logFilters = { date: null, level: null, category: null, search: '' };
-  state.logPagination = { offset: 0, limit: 100 };
-
-  // Initial load
-  loadLogEntries();
-  loadLogStats();
-  loadCsvFiles();
-
-  // CSV section toggle
-  const csvToggle = document.getElementById('csv-section-toggle');
-  const csvBody = document.getElementById('csv-section-body');
-  const csvIcon = document.getElementById('csv-toggle-icon');
-  if (csvToggle && csvBody) {
-    csvToggle.addEventListener('click', () => {
-      csvBody.classList.toggle('hidden');
-      csvIcon?.classList.toggle('rotate-90');
-    });
-  }
-
-  // CSV preview close button
-  document.getElementById('csv-preview-close')?.addEventListener('click', () => {
-    hideEl('csv-preview-panel');
-    currentPreviewPath = '';
-  });
-
-  // Filter controls
-  const { date: dateEl, level: levelEl, category: catEl, search: searchEl } = getFilterEls();
-  const clearBtn = document.getElementById('clear-filters-btn');
-  const syncBtn = document.getElementById('sync-logs-btn');
-  const prevBtn = document.getElementById('prev-page-btn');
-  const nextBtn = document.getElementById('next-page-btn');
-
-  if (dateEl) dateEl.addEventListener('change', applyFilters);
-  if (levelEl) levelEl.addEventListener('change', applyFilters);
-  if (catEl) catEl.addEventListener('change', applyFilters);
-
-  // Debounced search
-  if (searchEl) {
-    searchEl.addEventListener('input', debounce(applyFilters, 300));
-  }
-
-  if (clearBtn) clearBtn.addEventListener('click', clearFilters);
-  if (syncBtn) syncBtn.addEventListener('click', syncLogs);
-
-  if (prevBtn) {
-    prevBtn.addEventListener('click', () => {
-      state.logPagination.offset = Math.max(
-        0,
-        state.logPagination.offset - state.logPagination.limit,
-      );
-      loadLogEntries();
-    });
-  }
-
-  if (nextBtn) {
-    nextBtn.addEventListener('click', () => {
-      state.logPagination.offset += state.logPagination.limit;
-      loadLogEntries();
-    });
-  }
-}
diff --git a/app/static/js/modules/notify.js b/app/static/js/modules/notify.js
deleted file mode 100644
index e121a5b..0000000
--- a/app/static/js/modules/notify.js
+++ /dev/null
@@ -1,25 +0,0 @@
-/**
- * Toast notification system.
- */
-
-/**
- * @param {string} message
- * @param {'info' | 'error' | 'success'} [type]
- */
-export function showNotification(message, type = 'info') {
-  const notification = document.createElement('div');
-  notification.className = `fixed top-4 right-4 px-6 py-3 rounded-md shadow-lg z-50 transition-opacity duration-300 ${
-    type === 'error'
-      ? 'bg-red-500 text-white'
-      : type === 'success'
-        ? 'bg-green-500 text-white'
-        : 'bg-nlr-blue text-white'
-  }`;
-  notification.textContent = message;
-  document.body.appendChild(notification);
-
-  setTimeout(() => {
-    notification.classList.add('opacity-0');
-    setTimeout(() => notification.remove(), 300);
-  }, 5000);
-}
diff --git a/app/static/js/modules/settings.js b/app/static/js/modules/settings.js
deleted file mode 100644
index 06c3ea5..0000000
--- a/app/static/js/modules/settings.js
+++ /dev/null
@@ -1,402 +0,0 @@
-import { apiGet, apiPost, apiPut } from './api.js';
-import { appendText, setText, showEl, withLoadingButton } from './dom.js';
-import { showNotification } from './notify.js';
-/**
- * Settings page functionality.
- */
-import state from './state.js';
-
-const AWS_REGION_OPTIONS = new Set([
-  'us-west-2',
-  'us-west-1',
-  'us-east-1',
-  'us-east-2',
-  'us-gov-west-1',
-  'us-gov-east-1',
-]);
-
-function getAwsRegion() {
-  const select = /** @type {HTMLSelectElement | null} */ (
-    document.getElementById('aws-region-select')
-  );
-  if (select?.value === 'other') {
-    const custom = /** @type {HTMLInputElement | null} */ (
-      document.getElementById('aws-region-custom')
-    );
-    return custom?.value.trim() || '';
-  }
-  return select?.value || 'us-west-2';
-}
-
-/**
- * @param {string} region
- */
-function setAwsRegion(region) {
-  const select = /** @type {HTMLSelectElement | null} */ (
-    document.getElementById('aws-region-select')
-  );
-  const customInput = document.getElementById('aws-region-custom');
-  const helpText = document.getElementById('aws-region-help');
-
-  if (!select || !customInput || !helpText) return;
-
-  if (AWS_REGION_OPTIONS.has(region)) {
-    select.value = region;
-    customInput.classList.add('hidden');
-    helpText.classList.add('hidden');
-    /** @type {HTMLInputElement} */ (customInput).value = '';
-  } else {
-    select.value = 'other';
-    /** @type {HTMLInputElement} */ (customInput).value = region;
-    customInput.classList.remove('hidden');
-    helpText.classList.remove('hidden');
-  }
-}
-
-export function initSettings() {
-  const form = document.getElementById('settings-form');
-  if (!form) return;
-
-  document.getElementById('aws-region-select')?.addEventListener('change', (e) => {
-    const customInput = document.getElementById('aws-region-custom');
-    const helpText = document.getElementById('aws-region-help');
-    if (/** @type {HTMLSelectElement} */ (e.target).value === 'other') {
-      customInput?.classList.remove('hidden');
-      helpText?.classList.remove('hidden');
-      /** @type {HTMLInputElement} */ (customInput)?.focus();
-    } else {
-      customInput?.classList.add('hidden');
-      helpText?.classList.add('hidden');
-      if (customInput) /** @type {HTMLInputElement} */ (customInput).value = '';
-    }
-  });
-
-  loadCurrentSettings();
-  loadAwsProfiles();
-  loadVersionInfo();
-  loadCacheStats();
-
-  form.addEventListener('submit', async (e) => {
-    e.preventDefault();
-    await saveSettings();
-  });
-
-  document.getElementById('test-connection-btn')?.addEventListener('click', testConnection);
-  document.getElementById('check-updates-btn')?.addEventListener('click', checkForUpdates);
-  document.getElementById('run-update-btn')?.addEventListener('click', runUpdate);
-  document.getElementById('reset-settings-btn')?.addEventListener('click', resetSettings);
-  document.getElementById('clear-cache-btn')?.addEventListener('click', clearBrowserCache);
-  document.getElementById('sync-cache-btn')?.addEventListener('click', syncCacheWithAws);
-  document.getElementById('invalidate-cache-btn')?.addEventListener('click', invalidateUploadCache);
-}
-
-async function loadCurrentSettings() {
-  try {
-    const settings = await apiGet('/api/settings');
-
-    setAwsRegion(settings.aws_region || 'us-west-2');
-
-    const s3Bucket = /** @type {HTMLInputElement | null} */ (document.getElementById('s3-bucket'));
-    if (s3Bucket) s3Bucket.value = settings.s3_bucket || '';
-
-    const defaultFolder = /** @type {HTMLInputElement | null} */ (
-      document.getElementById('default-folder')
-    );
-    if (defaultFolder) defaultFolder.value = settings.default_upload_folder || '';
-
-    state.currentAwsProfile = settings.aws_profile;
-  } catch (_error) {
-    showNotification('Failed to load settings', 'error');
-  }
-}
-
-async function loadAwsProfiles() {
-  try {
-    const data = await apiGet('/api/settings/profiles');
-
-    const select = /** @type {HTMLSelectElement | null} */ (document.getElementById('aws-profile'));
-    if (!select) return;
-
-    select.innerHTML = data.profiles
-      .map((/** @type {string} */ profile) => `<option value="${profile}">${profile}</option>`)
-      .join('');
-
-    if (state.currentAwsProfile) {
-      select.value = state.currentAwsProfile;
-    }
-  } catch (_error) {
-    showNotification('Failed to load AWS profiles', 'error');
-  }
-}
-
-async function loadVersionInfo() {
-  try {
-    const data = await apiGet('/api/settings/version');
-
-    setText('git-branch', data.branch || '-');
-    setText('git-commit', data.commit || '-');
-    setText('git-date', data.last_updated || '-');
-    setText('pkg-version', data.version || '-');
-
-    let versionText = data.version || '0.0.0';
-    if (data.commit) {
-      versionText += ` (${data.commit})`;
-    }
-    setText('version-info', versionText);
-  } catch (error) {
-    console.error('Failed to load version info:', error);
-  }
-}
-
-async function saveSettings() {
-  const settings = {
-    aws_profile: /** @type {HTMLSelectElement} */ (document.getElementById('aws-profile'))?.value,
-    aws_region: getAwsRegion(),
-    s3_bucket: /** @type {HTMLInputElement} */ (document.getElementById('s3-bucket'))?.value,
-    default_upload_folder: /** @type {HTMLInputElement} */ (
-      document.getElementById('default-folder')
-    )?.value,
-  };
-
-  try {
-    await apiPut('/api/settings', settings);
-    showNotification('Settings saved successfully', 'success');
-  } catch (error) {
-    showNotification(/** @type {Error} */ (error).message, 'error');
-  }
-}
-
-async function testConnection() {
-  const btn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('test-connection-btn')
-  );
-  const status = document.getElementById('connection-status');
-  if (!btn || !status) return;
-
-  status.textContent = 'Testing connection...';
-  status.className = 'mt-1 text-sm text-gray-500';
-
-  const settings = {
-    aws_profile: /** @type {HTMLSelectElement} */ (document.getElementById('aws-profile'))?.value,
-    aws_region: getAwsRegion(),
-    s3_bucket: /** @type {HTMLInputElement} */ (document.getElementById('s3-bucket'))?.value,
-  };
-
-  await withLoadingButton(btn, 'Testing...', async () => {
-    try {
-      const data = await apiPost('/api/settings/validate', settings);
-      status.textContent = data.success ? data.message : data.error;
-      status.className = `mt-1 text-sm ${data.success ? 'text-green-600' : 'text-red-600'}`;
-    } catch (error) {
-      status.textContent = /** @type {Error} */ (error).message;
-      status.className = 'mt-1 text-sm text-red-600';
-    }
-  });
-}
-
-async function checkForUpdates() {
-  const btn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('check-updates-btn')
-  );
-  const status = document.getElementById('update-status');
-  const updateBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('run-update-btn')
-  );
-  if (!btn || !status) return;
-
-  await withLoadingButton(btn, 'Checking...', async () => {
-    try {
-      const data = await apiGet('/api/settings/check-updates');
-
-      if (data.error) {
-        status.textContent = `Error: ${data.error}`;
-        status.className = 'text-sm text-red-600';
-      } else if (data.updates_available) {
-        status.textContent = 'Updates available! Click "Update Application" to install.';
-        status.className = 'text-sm text-nlr-yellow font-medium';
-        if (updateBtn) updateBtn.disabled = false;
-      } else if (data.up_to_date) {
-        status.textContent = 'Application is up to date.';
-        status.className = 'text-sm text-green-600';
-      } else {
-        status.textContent = 'Could not determine update status.';
-        status.className = 'text-sm text-gray-600';
-      }
-    } catch (error) {
-      status.textContent = /** @type {Error} */ (error).message;
-      status.className = 'text-sm text-red-600';
-    }
-  });
-}
-
-async function runUpdate() {
-  const btn = /** @type {HTMLButtonElement | null} */ (document.getElementById('run-update-btn'));
-  const status = document.getElementById('update-status');
-  if (!btn || !status) return;
-
-  status.textContent = 'Running update...';
-  showEl('update-log');
-  setText('update-output', 'Starting update...\n');
-
-  await withLoadingButton(btn, 'Updating...', async () => {
-    try {
-      const data = await apiPost('/api/settings/update');
-
-      let output = '';
-
-      if (data.results.git_pull) {
-        output += '=== Git Pull ===\n';
-        output += data.results.git_pull.success ? '[SUCCESS]\n' : '[FAILED]\n';
-        output += `${data.results.git_pull.output}\n\n`;
-      }
-
-      if (data.results.pip_install) {
-        output += '=== Pip Install ===\n';
-        output += data.results.pip_install.success ? '[SUCCESS]\n' : '[FAILED]\n';
-        output += `${data.results.pip_install.output}\n\n`;
-      }
-
-      if (data.results.modaq_toolkit) {
-        output += '=== MODAQ Toolkit Update ===\n';
-        output += data.results.modaq_toolkit.success ? '[SUCCESS]\n' : '[FAILED]\n';
-        output += `${data.results.modaq_toolkit.output}\n`;
-      }
-
-      setText('update-output', output);
-
-      if (data.success) {
-        status.textContent = 'Update completed! Restart the application to apply changes.';
-        status.className = 'text-sm text-green-600 font-medium';
-        showNotification('Update completed! Please restart the application.', 'success');
-      } else {
-        status.textContent = 'Update completed with some errors. Check the log below.';
-        status.className = 'text-sm text-yellow-600';
-      }
-
-      loadVersionInfo();
-    } catch (error) {
-      status.textContent = /** @type {Error} */ (error).message;
-      status.className = 'text-sm text-red-600';
-      appendText('update-output', `\nError: ${/** @type {Error} */ (error).message}`);
-    }
-  });
-}
-
-async function resetSettings() {
-  if (!confirm('Are you sure you want to reset all settings to defaults?')) {
-    return;
-  }
-
-  try {
-    await apiPut('/api/settings', {
-      aws_profile: 'default',
-      aws_region: 'us-west-2',
-      s3_bucket: '',
-      default_upload_folder: '',
-    });
-
-    loadCurrentSettings();
-    showNotification('Settings reset to defaults', 'success');
-  } catch (error) {
-    showNotification(/** @type {Error} */ (error).message, 'error');
-  }
-}
-
-function clearBrowserCache() {
-  if (
-    !confirm(
-      'Are you sure you want to clear the browser cache? This will forget your last used folder and other local preferences.',
-    )
-  ) {
-    return;
-  }
-
-  try {
-    localStorage.removeItem('lastUploadFolder');
-    showNotification('Browser cache cleared', 'success');
-  } catch (error) {
-    showNotification(`Failed to clear cache: ${/** @type {Error} */ (error).message}`, 'error');
-  }
-}
-
-async function loadCacheStats() {
-  try {
-    const data = await apiGet('/api/settings/cache/stats');
-
-    if (data.success && data.stats) {
-      const stats = data.stats;
-
-      setText('cache-total', stats.total_entries || 0);
-      setText('cache-exists', stats.exists_count || 0);
-      setText('cache-deleted', stats.not_exists_count || 0);
-
-      if (stats.last_full_sync) {
-        setText('cache-last-sync', new Date(stats.last_full_sync).toLocaleString());
-      } else {
-        setText('cache-last-sync', 'Never');
-      }
-    }
-  } catch (error) {
-    console.error('Failed to load cache stats:', error);
-  }
-}
-
-async function syncCacheWithAws() {
-  const btn = /** @type {HTMLButtonElement | null} */ (document.getElementById('sync-cache-btn'));
-  const status = document.getElementById('sync-status');
-  if (!btn || !status) return;
-
-  status.classList.remove('hidden');
-  status.textContent = 'Fetching file list from S3...';
-  status.className = 'mt-2 text-sm text-gray-600';
-
-  await withLoadingButton(btn, 'Syncing...', async () => {
-    try {
-      const data = await apiPost('/api/settings/cache/sync');
-
-      if (data.success) {
-        status.textContent = data.message;
-        status.className = 'mt-2 text-sm text-green-600';
-        showNotification(data.message, 'success');
-        loadCacheStats();
-      } else {
-        status.textContent = `Error: ${data.error}`;
-        status.className = 'mt-2 text-sm text-red-600';
-        showNotification(data.error, 'error');
-      }
-    } catch (error) {
-      status.textContent = `Error: ${/** @type {Error} */ (error).message}`;
-      status.className = 'mt-2 text-sm text-red-600';
-      showNotification(/** @type {Error} */ (error).message, 'error');
-    }
-  });
-}
-
-async function invalidateUploadCache() {
-  if (
-    !confirm(
-      'Are you sure you want to clear the upload cache? This will delete all cached file records for the current bucket. The next upload will need to re-check all files against S3.',
-    )
-  ) {
-    return;
-  }
-
-  const btn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('invalidate-cache-btn')
-  );
-
-  await withLoadingButton(btn, 'Clearing...', async () => {
-    try {
-      const data = await apiPost('/api/settings/cache/invalidate');
-
-      if (data.success) {
-        showNotification(data.message, 'success');
-        loadCacheStats();
-      } else {
-        showNotification(data.error || 'Failed to clear cache', 'error');
-      }
-    } catch (error) {
-      showNotification(/** @type {Error} */ (error).message, 'error');
-    }
-  });
-}
diff --git a/app/static/js/modules/sorting-helpers.js b/app/static/js/modules/sorting-helpers.js
deleted file mode 100644
index 4ce1d70..0000000
--- a/app/static/js/modules/sorting-helpers.js
+++ /dev/null
@@ -1,40 +0,0 @@
-/**
- * Table sorting helpers: toggle column direction and update header indicators.
- */
-
-/**
- * Toggle sort direction on a column config object.
- * @param {{ column: string, ascending: boolean }} config
- * @param {string} column
- */
-export function toggleSort(config, column) {
-  if (config.column === column) {
-    config.ascending = !config.ascending;
-  } else {
-    config.column = column;
-    config.ascending = true;
-  }
-}
-
-/**
- * Update sort indicator arrows in table headers.
- * @param {string} headerSelector  - e.g. `'[data-sort]'`
- * @param {string} indicatorSelector - e.g. `'.sort-indicator'`
- * @param {string} dataKey - dataset key, e.g. `'sort'` or `'fileSort'`
- * @param {string} currentColumn
- * @param {boolean} ascending
- */
-export function updateSortIndicators(
-  headerSelector,
-  indicatorSelector,
-  dataKey,
-  currentColumn,
-  ascending,
-) {
-  for (const th of document.querySelectorAll(headerSelector)) {
-    const indicator = th.querySelector(indicatorSelector);
-    if (!indicator) continue;
-    const col = /** @type {HTMLElement} */ (th).dataset[dataKey];
-    indicator.textContent = col === currentColumn ? (ascending ? ' \u25B2' : ' \u25BC') : '';
-  }
-}
diff --git a/app/static/js/modules/state.js b/app/static/js/modules/state.js
deleted file mode 100644
index 1febefd..0000000
--- a/app/static/js/modules/state.js
+++ /dev/null
@@ -1,75 +0,0 @@
-/**
- * Centralized mutable state for the modaq_upload.
- * Replaces all global `let` variables and `window.*` properties.
- */
-const state = {
-  /** @type {string | null} */
-  currentJobId: null,
-
-  /** @type {EventSource | null} */
-  eventSource: null,
-
-  /** @type {string | null} */
-  selectedFolderPath: null,
-
-  /** Current upload step (1-4) */
-  currentStep: 1,
-
-  /** S3 file browser current prefix */
-  currentPrefix: '',
-
-  /** @type {{ version?: string, commit?: string, branch?: string } | null} */
-  appVersionData: null,
-
-  /** @type {string | undefined} */
-  currentAwsProfile: undefined,
-
-  /** @type {string[]} */
-  scanFilePaths: [],
-
-  /** @type {Array<{ path: string, filename: string, size: number, mtime?: number, already_uploaded: boolean }>} */
-  scanFileStatuses: [],
-
-  /** Total size of all scanned files in bytes */
-  scanTotalSize: 0,
-
-  /** @type {string | null} */
-  scanFolderPath: null,
-
-  /** @type {string | null} */
-  scanJobId: null,
-
-  /** Sort configuration for the review table */
-  reviewSortConfig: { column: 'filename', ascending: true },
-
-  /** @type {Array<{ name: string, size: number, mtime: number }>} */
-  browserFiles: [],
-
-  /** Sort configuration for the folder browser file table */
-  browserFileSortConfig: { column: 'name', ascending: true },
-
-  /** @type {Array<{ relative_path: string, files: any[], total_files: number, already_uploaded: number, all_uploaded: boolean, error: string | null }>} */
-  browserScanResults: [],
-
-  /** @type {EventSource | null} Browser scan SSE connection (separate from main eventSource) */
-  browserScanEventSource: null,
-
-  /** @type {string | null} Browser scan job ID */
-  browserScanJobId: null,
-
-  /** Whether the browser scan has completed */
-  browserScanComplete: false,
-
-  /** Log viewer filter state */
-  logFilters: {
-    /** @type {string | null} */ date: null,
-    /** @type {string | null} */ level: null,
-    /** @type {string | null} */ category: null,
-    /** @type {string} */ search: '',
-  },
-
-  /** Log viewer pagination state */
-  logPagination: { offset: 0, limit: 100 },
-};
-
-export default state;
diff --git a/app/static/js/modules/stepper.js b/app/static/js/modules/stepper.js
deleted file mode 100644
index bce8cdd..0000000
--- a/app/static/js/modules/stepper.js
+++ /dev/null
@@ -1,83 +0,0 @@
-/**
- * Upload step indicator management.
- */
-import { setText } from './dom.js';
-import { showNotification } from './notify.js';
-import state from './state.js';
-
-export const UPLOAD_STEPS = {
-  1: { name: 'Select', description: 'Select files or a folder to upload' },
-  2: {
-    name: 'Review',
-    description: 'Review files found - click Continue to upload, or Back to select different files',
-  },
-  3: { name: 'Upload', description: 'Validating and uploading files...' },
-  4: { name: 'Complete', description: 'Upload complete!' },
-};
-
-/**
- * Set the current step in the upload flow.
- * @param {number} step
- */
-export function setUploadStep(step) {
-  state.currentStep = step;
-  const stepsContainer = document.getElementById('upload-steps');
-  if (!stepsContainer) return;
-
-  for (let i = 1; i <= 4; i++) {
-    const stepEl = stepsContainer.querySelector(`[data-step="${i}"]`);
-    if (!stepEl) continue;
-
-    stepEl.classList.remove('completed', 'active');
-
-    if (i < step) {
-      stepEl.classList.add('completed');
-    } else if (i === step) {
-      stepEl.classList.add('active');
-    }
-  }
-
-  const connectors = stepsContainer.querySelectorAll('.step-connector');
-  connectors.forEach((connector, index) => {
-    /** @type {HTMLElement} */ (connector).style.backgroundColor =
-      index < step - 1 ? '#5D9732' : '#D1D5DB';
-  });
-
-  if (UPLOAD_STEPS[step]) {
-    setText('step-description', UPLOAD_STEPS[step].description);
-  }
-}
-
-/**
- * Show the upload steps indicator and set the current step.
- * @param {number} step
- */
-export function showUploadSteps(step) {
-  setUploadStep(step);
-}
-
-/**
- * Reset the upload steps indicator to step 1.
- */
-export function hideUploadSteps() {
-  setUploadStep(1);
-}
-
-/**
- * Navigate to a specific step (for going back).
- * Uses dynamic import to avoid circular dependency with upload-control.
- * @param {number} targetStep
- */
-export async function goToStep(targetStep) {
-  if (targetStep >= state.currentStep) return;
-
-  if (targetStep === 1 && state.currentStep <= 2) {
-    const { resetUpload } = await import('./upload-control.js');
-    resetUpload();
-    return;
-  }
-
-  if (state.currentStep >= 3) {
-    showNotification('Cannot go back during or after upload', 'error');
-  }
-}
diff --git a/app/static/js/modules/upload-control.js b/app/static/js/modules/upload-control.js
deleted file mode 100644
index 40d1b80..0000000
--- a/app/static/js/modules/upload-control.js
+++ /dev/null
@@ -1,54 +0,0 @@
-import { resetAnalysisState } from './analysis.js';
-/**
- * Cancel and reset operations for uploads.
- */
-import { apiPost } from './api.js';
-import { hideEl, showEl } from './dom.js';
-import { showNotification } from './notify.js';
-import state from './state.js';
-import { hideUploadSteps } from './stepper.js';
-
-export async function cancelUpload() {
-  // Cancel scan job if active
-  if (state.scanJobId) {
-    try {
-      await apiPost(`/api/upload/cancel/${state.scanJobId}`);
-    } catch (_error) {
-      // Scan may have already finished
-    }
-  }
-
-  if (!state.currentJobId) return;
-
-  try {
-    await apiPost(`/api/upload/cancel/${state.currentJobId}`);
-    if (state.eventSource) state.eventSource.close();
-    showNotification('Upload cancelled', 'info');
-  } catch (_error) {
-    showNotification('Failed to cancel upload', 'error');
-  }
-}
-
-export function resetUpload() {
-  state.currentJobId = null;
-  if (state.eventSource) {
-    state.eventSource.close();
-    state.eventSource = null;
-  }
-
-  resetAnalysisState();
-  hideUploadSteps();
-
-  showEl('folder-browser-panel');
-  hideEl('upload-section');
-  hideEl('completion-section');
-  hideEl('scan-results-section');
-  hideEl('confirm-upload-modal');
-
-  state.selectedFolderPath = null;
-  state.scanFilePaths = [];
-  state.scanFileStatuses = [];
-  state.scanTotalSize = 0;
-  state.scanFolderPath = null;
-  state.scanJobId = null;
-}
diff --git a/app/static/js/modules/upload-exec.js b/app/static/js/modules/upload-exec.js
deleted file mode 100644
index 85736f8..0000000
--- a/app/static/js/modules/upload-exec.js
+++ /dev/null
@@ -1,226 +0,0 @@
-/**
- * Upload execution: progress tracking and completion summary.
- * Completion table is paginated (100 rows per page) for 20K+ file performance.
- */
-import { hideEl, setText, showEl } from './dom.js';
-import { formatDuration, formatEta } from './formatters.js';
-import { fileIcon } from './icons.js';
-import { showNotification } from './notify.js';
-import { setUploadStep } from './stepper.js';
-
-const COMPLETION_PAGE_SIZE = 100;
-
-/** @type {any} */
-let lastCompletedJob = null;
-
-/** Current page (0-indexed) of the completion table. */
-let completionPage = 0;
-
-/**
- * @param {any} job
- */
-export function updateProgressUI(job) {
-  setText('progress-percent', job.progress_percent.toFixed(1));
-  setText('files-completed', job.files_completed);
-  setText('files-total', job.total_files);
-  setText('bytes-uploaded', job.uploaded_bytes_formatted);
-  setText('bytes-total', job.total_bytes_formatted);
-  setText('eta', formatEta(job.eta_seconds));
-
-  const progressBar = /** @type {HTMLElement | null} */ (document.getElementById('progress-bar'));
-  if (progressBar) progressBar.style.width = `${job.progress_percent}%`;
-}
-
-/**
- * @param {any} job
- */
-export function showCompletionSummary(job) {
-  lastCompletedJob = job;
-  completionPage = 0;
-  setUploadStep(4);
-
-  hideEl('upload-section');
-  showEl('completion-section');
-
-  // Use pre-computed counts from backend (avoids 3 filter passes over 20K files)
-  const completed =
-    job.files_uploaded ??
-    job.files.filter((/** @type {any} */ f) => f.status === 'completed').length;
-  const skipped =
-    job.files_skipped ?? job.files.filter((/** @type {any} */ f) => f.status === 'skipped').length;
-  const failed =
-    job.files_failed ?? job.files.filter((/** @type {any} */ f) => f.status === 'failed').length;
-
-  setText('completed-count', completed);
-  setText('skipped-count', skipped);
-  setText('failed-count', failed);
-  setText('total-uploaded-size', job.successfully_uploaded_bytes_formatted || '-');
-  setText('total-upload-time', job.total_upload_duration_formatted || '-');
-  setText(
-    'avg-upload-speed',
-    job.average_upload_speed_mbps ? `${job.average_upload_speed_mbps} Mbps` : '-',
-  );
-
-  // Single pass for average per-file duration (not pre-computed by backend)
-  let durationSum = 0;
-  let durationCount = 0;
-  for (const f of job.files) {
-    if (f.status === 'completed' && f.upload_duration_seconds) {
-      durationSum += f.upload_duration_seconds;
-      durationCount++;
-    }
-  }
-  setText('avg-file-time', durationCount > 0 ? formatDuration(durationSum / durationCount) : '-');
-
-  // Render first page and wire up pagination
-  renderCompletionPage();
-  wireCompletionPagination();
-
-  if (failed === 0) {
-    showNotification('Upload completed successfully!', 'success');
-  } else {
-    showNotification(`Upload completed with ${failed} failed files`, 'error');
-  }
-}
-
-/**
- * Render the current page of the completion file table.
- */
-function renderCompletionPage() {
-  if (!lastCompletedJob) return;
-
-  const files = lastCompletedJob.files;
-  const totalPages = Math.max(1, Math.ceil(files.length / COMPLETION_PAGE_SIZE));
-  const start = completionPage * COMPLETION_PAGE_SIZE;
-  const end = Math.min(start + COMPLETION_PAGE_SIZE, files.length);
-  const pageFiles = files.slice(start, end);
-
-  const tbody = document.getElementById('completion-file-list');
-  if (tbody) {
-    tbody.innerHTML = pageFiles
-      .map((/** @type {any} */ file) => {
-        let statusBadge;
-        let statusClass;
-        if (file.status === 'completed') {
-          statusBadge = 'Uploaded';
-          statusClass = 'bg-green-100 text-green-800';
-        } else if (file.status === 'skipped') {
-          statusBadge = 'Skipped';
-          statusClass = 'bg-yellow-100 text-yellow-800';
-        } else if (file.status === 'failed') {
-          statusBadge = 'Failed';
-          statusClass = 'bg-red-100 text-red-800';
-        } else {
-          statusBadge = file.status;
-          statusClass = 'bg-gray-100 text-gray-800';
-        }
-
-        const duration = file.upload_duration_seconds
-          ? formatDuration(file.upload_duration_seconds)
-          : '-';
-        const speed = file.upload_speed_mbps ? `${file.upload_speed_mbps} Mbps` : '-';
-
-        return `
-                <tr>
-                    <td class="px-4 py-3">
-                        <div class="flex items-center">
-                            ${fileIcon('h-4 w-4 text-gray-400 mr-2')}
-                            <span class="text-sm text-gray-900 truncate" title="${file.filename}">${file.filename}</span>
-                        </div>
-                    </td>
-                    <td class="px-4 py-3 text-sm text-gray-500 truncate" title="${file.s3_path || ''}">${file.s3_path || '-'}</td>
-                    <td class="px-4 py-3 text-sm text-gray-500">${file.file_size_formatted}</td>
-                    <td class="px-4 py-3 text-sm text-gray-500">${duration}</td>
-                    <td class="px-4 py-3 text-sm text-gray-500">${speed}</td>
-                    <td class="px-4 py-3">
-                        <span class="px-2 py-1 text-xs rounded-full ${statusClass}">${statusBadge}</span>
-                    </td>
-                </tr>
-            `;
-      })
-      .join('');
-  }
-
-  // Update pagination controls
-  setText('completion-page-info', `Page ${completionPage + 1} of ${totalPages}`);
-
-  const prevBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('completion-prev-btn')
-  );
-  const nextBtn = /** @type {HTMLButtonElement | null} */ (
-    document.getElementById('completion-next-btn')
-  );
-  if (prevBtn) prevBtn.disabled = completionPage === 0;
-  if (nextBtn) nextBtn.disabled = completionPage >= totalPages - 1;
-}
-
-/**
- * Wire up pagination button click handlers.
- */
-function wireCompletionPagination() {
-  const prevBtn = document.getElementById('completion-prev-btn');
-  const nextBtn = document.getElementById('completion-next-btn');
-
-  if (prevBtn) {
-    prevBtn.onclick = () => {
-      if (completionPage > 0) {
-        completionPage--;
-        renderCompletionPage();
-      }
-    };
-  }
-
-  if (nextBtn) {
-    nextBtn.onclick = () => {
-      if (!lastCompletedJob) return;
-      const totalPages = Math.ceil(lastCompletedJob.files.length / COMPLETION_PAGE_SIZE);
-      if (completionPage < totalPages - 1) {
-        completionPage++;
-        renderCompletionPage();
-      }
-    };
-  }
-}
-
-/**
- * Download the upload summary as a CSV file.
- */
-export function downloadSummaryCSV() {
-  if (!lastCompletedJob || !lastCompletedJob.files) {
-    showNotification('No upload data available', 'error');
-    return;
-  }
-
-  const headers = ['Filename', 'Size', 'S3 Path', 'Status', 'Duration', 'Speed'];
-  const rows = lastCompletedJob.files.map((/** @type {any} */ file) => {
-    const duration = file.upload_duration_seconds
-      ? formatDuration(file.upload_duration_seconds)
-      : '';
-    const speed = file.upload_speed_mbps ? `${file.upload_speed_mbps} Mbps` : '';
-    return [
-      file.filename,
-      file.file_size_formatted || '',
-      file.s3_path || '',
-      file.status,
-      duration,
-      speed,
-    ];
-  });
-
-  const csvContent = [
-    headers.join(','),
-    ...rows.map((/** @type {string[]} */ row) =>
-      row.map((/** @type {string} */ cell) => `"${String(cell).replace(/"/g, '""')}"`).join(','),
-    ),
-  ].join('\n');
-
-  const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
-  const url = URL.createObjectURL(blob);
-  const link = document.createElement('a');
-  link.href = url;
-  const now = new Date();
-  const pad = (/** @type {number} */ n) => String(n).padStart(2, '0');
-  link.download = `upload-summary-${now.toISOString().slice(0, 10)}-${pad(now.getHours())}${pad(now.getMinutes())}.csv`;
-  link.click();
-  URL.revokeObjectURL(url);
-}
diff --git a/app/static/js/modules/upload-init.js b/app/static/js/modules/upload-init.js
deleted file mode 100644
index 28855ba..0000000
--- a/app/static/js/modules/upload-init.js
+++ /dev/null
@@ -1,53 +0,0 @@
-import { checkForActiveJob } from './analysis.js';
-import { apiPost } from './api.js';
-import { hideEl, showEl } from './dom.js';
-import { initFolderBrowser, showConfirmModal, startCombinedUpload } from './folder-browser.js';
-/**
- * Upload page initialization and event wiring.
- */
-import state from './state.js';
-import { setUploadStep } from './stepper.js';
-import { cancelUpload, resetUpload } from './upload-control.js';
-import { downloadSummaryCSV } from './upload-exec.js';
-
-export function initUpload() {
-  const panel = document.getElementById('folder-browser-panel');
-  if (!panel) return;
-
-  initFolderBrowser();
-
-  setUploadStep(1);
-  checkForActiveJob();
-
-  document.getElementById('cancel-upload-btn')?.addEventListener('click', cancelUpload);
-  document.getElementById('upload-more-btn')?.addEventListener('click', resetUpload);
-  document.getElementById('download-csv-btn')?.addEventListener('click', downloadSummaryCSV);
-
-  document.getElementById('continue-upload-btn')?.addEventListener('click', showConfirmModal);
-  document.getElementById('confirm-upload-btn')?.addEventListener('click', startCombinedUpload);
-
-  document.getElementById('cancel-scan-btn')?.addEventListener('click', async () => {
-    // Cancel active scan job if running
-    if (state.scanJobId) {
-      try {
-        await apiPost(`/api/upload/cancel/${state.scanJobId}`);
-      } catch (_error) {
-        // Scan may have already finished
-      }
-      if (state.eventSource) {
-        state.eventSource.close();
-        state.eventSource = null;
-      }
-      state.scanJobId = null;
-    }
-
-    hideEl('scan-results-section');
-    showEl('folder-browser-panel');
-    state.selectedFolderPath = null;
-    state.scanFilePaths = [];
-    state.scanFileStatuses = [];
-    state.scanTotalSize = 0;
-    state.scanFolderPath = null;
-    setUploadStep(1);
-  });
-}

From 5c4d805e934789684a371277ec0fb51f8d2fcf5c Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Tue, 17 Feb 2026 17:05:37 -0700
Subject: [PATCH 098/173] Refactor: Remove legacy js configuration

---
 biome.json       | 39 ---------------------------------------
 jsconfig.json    | 14 --------------
 package.json     | 21 ---------------------
 vitest.config.js | 13 -------------
 4 files changed, 87 deletions(-)
 delete mode 100644 biome.json
 delete mode 100644 jsconfig.json
 delete mode 100644 package.json
 delete mode 100644 vitest.config.js

diff --git a/biome.json b/biome.json
deleted file mode 100644
index 0e9c777..0000000
--- a/biome.json
+++ /dev/null
@@ -1,39 +0,0 @@
-{
-  "$schema": "https://biomejs.dev/schemas/1.9.0/schema.json",
-  "organizeImports": {
-    "enabled": true
-  },
-  "formatter": {
-    "enabled": true,
-    "indentStyle": "space",
-    "indentWidth": 2,
-    "lineWidth": 100
-  },
-  "javascript": {
-    "formatter": {
-      "quoteStyle": "single",
-      "semicolons": "always"
-    }
-  },
-  "linter": {
-    "enabled": true,
-    "rules": {
-      "recommended": true,
-      "correctness": {
-        "noUnusedVariables": "warn",
-        "noUnusedImports": "warn"
-      },
-      "suspicious": {
-        "noExplicitAny": "off"
-      },
-      "style": {
-        "noParameterAssign": "off",
-        "useConst": "error"
-      }
-    }
-  },
-  "files": {
-    "include": ["app/static/js/**/*.js"],
-    "ignore": ["node_modules/", "tests/"]
-  }
-}
diff --git a/jsconfig.json b/jsconfig.json
deleted file mode 100644
index 187ef93..0000000
--- a/jsconfig.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "compilerOptions": {
-        "checkJs": true,
-        "noEmit": true,
-        "strict": false,
-        "target": "ES2022",
-        "module": "ES2022",
-        "moduleResolution": "bundler",
-        "lib": ["ES2022", "DOM", "DOM.Iterable"],
-        "skipLibCheck": true
-    },
-    "include": ["app/static/js/**/*.js"],
-    "exclude": ["node_modules", "tests"]
-}
diff --git a/package.json b/package.json
deleted file mode 100644
index 611fc07..0000000
--- a/package.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-  "private": true,
-  "name": "modaq-upload",
-  "description": "Frontend js for modaq_upload flask app",
-  "scripts": {
-    "lint": "biome check app/static/js/",
-    "lint:fix": "biome check --write app/static/js/",
-    "typecheck": "tsc -p jsconfig.json",
-    "test": "vitest run",
-    "test:watch": "vitest",
-    "test:coverage": "vitest run --coverage",
-    "check": "biome check app/static/js/ && tsc -p jsconfig.json && vitest run"
-  },
-  "devDependencies": {
-    "@biomejs/biome": "^1.9.0",
-    "@vitest/coverage-v8": "^2.1.0",
-    "jsdom": "^25.0.0",
-    "typescript": "^5.6.0",
-    "vitest": "^2.1.0"
-  }
-}
diff --git a/vitest.config.js b/vitest.config.js
deleted file mode 100644
index 53550f8..0000000
--- a/vitest.config.js
+++ /dev/null
@@ -1,13 +0,0 @@
-import { defineConfig } from 'vitest/config';
-
-export default defineConfig({
-    test: {
-        environment: 'jsdom',
-        include: ['tests/js/**/*.test.js'],
-        coverage: {
-            provider: 'v8',
-            include: ['app/static/js/**/*.js'],
-            reportsDirectory: 'htmlcov-js',
-        },
-    },
-});

From e134ed31fb2f63fb615a464be078480deb7683b6 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 09:27:10 -0700
Subject: [PATCH 099/173] Frontend: Add dev testing packages

---
 frontend/package-lock.json | 669 +++++++++++++++++++++++++++++++------
 frontend/package.json      |   3 +-
 2 files changed, 569 insertions(+), 103 deletions(-)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index c7aefc7..249a958 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -19,6 +19,7 @@
       "devDependencies": {
         "@eslint/js": "^9.39.1",
         "@tailwindcss/vite": "^4.1.18",
+        "@testing-library/dom": "^10.4.0",
         "@testing-library/jest-dom": "^6.9.1",
         "@testing-library/react": "^16.3.2",
         "@testing-library/user-event": "^14.6.1",
@@ -26,7 +27,7 @@
         "@types/react": "^19.2.7",
         "@types/react-dom": "^19.2.3",
         "@vitejs/plugin-react": "^5.1.1",
-        "@vitest/coverage-v8": "^4.0.18",
+        "@vitest/coverage-v8": "^3.2.4",
         "eslint": "^9.39.1",
         "eslint-plugin-react-hooks": "^7.0.1",
         "eslint-plugin-react-refresh": "^0.4.24",
@@ -46,6 +47,20 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/@ampproject/remapping": {
+      "version": "2.3.0",
+      "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz",
+      "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==",
+      "dev": true,
+      "license": "Apache-2.0",
+      "dependencies": {
+        "@jridgewell/gen-mapping": "^0.3.5",
+        "@jridgewell/trace-mapping": "^0.3.24"
+      },
+      "engines": {
+        "node": ">=6.0.0"
+      }
+    },
     "node_modules/@asamuzakjp/css-color": {
       "version": "4.1.2",
       "resolved": "https://registry.npmjs.org/@asamuzakjp/css-color/-/css-color-4.1.2.tgz",
@@ -1186,6 +1201,34 @@
         "url": "https://github.com/sponsors/nzakas"
       }
     },
+    "node_modules/@isaacs/cliui": {
+      "version": "8.0.2",
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@@ -4320,6 +4494,16 @@
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@@ -4421,6 +4594,13 @@
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       }
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+      "resolved": "https://registry.npmjs.org/package-json-from-dist/-/package-json-from-dist-1.0.1.tgz",
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@@ -4467,6 +4647,30 @@
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+        "minipass": "^5.0.0 || ^6.0.2 || ^7.0.0"
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+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
+      }
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@@ -4543,6 +4747,34 @@
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+        "ansi-styles": "^5.0.0",
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+      "license": "MIT",
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+      "funding": {
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@@ -4574,6 +4806,13 @@
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@@ -4780,6 +5019,19 @@
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+      "funding": {
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@@ -4804,6 +5056,103 @@
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+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
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+      "license": "MIT",
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+        "is-fullwidth-code-point": "^3.0.0",
+        "strip-ansi": "^6.0.1"
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+      "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
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+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/string-width-cjs/node_modules/strip-ansi": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
+      "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "ansi-regex": "^5.0.1"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
+    "node_modules/strip-ansi": {
+      "version": "7.1.2",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.2.tgz",
+      "integrity": "sha512-gmBGslpoQJtgnMAvOVqGZpEz9dyoKTCzy2nfz/n8aIFhN/jCE/rCmcxabB6jOOHV+0WNnylOxaxBQPSvcWklhA==",
+      "dev": true,
+      "license": "MIT",
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+      "engines": {
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+      "funding": {
+        "url": "https://github.com/chalk/strip-ansi?sponsor=1"
+      }
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+    "node_modules/strip-ansi-cjs": {
+      "name": "strip-ansi",
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
+      "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "ansi-regex": "^5.0.1"
+      },
+      "engines": {
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+    "node_modules/strip-ansi/node_modules/ansi-regex": {
+      "version": "6.2.2",
+      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.2.2.tgz",
+      "integrity": "sha512-Bq3SmSpyFHaWjPk8If9yc6svM8c56dB5BAtW4Qbw5jHTwwXXcTLoRMkpDJp6VL0XzlWaCHTXrkFURMYmD0sLqg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/ansi-regex?sponsor=1"
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+    },
     "node_modules/strip-indent": {
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       "resolved": "https://registry.npmjs.org/strip-indent/-/strip-indent-3.0.0.tgz",
@@ -4891,6 +5240,47 @@
         "url": "https://opencollective.com/webpack"
       }
     },
+    "node_modules/test-exclude": {
+      "version": "7.0.1",
+      "resolved": "https://registry.npmjs.org/test-exclude/-/test-exclude-7.0.1.tgz",
+      "integrity": "sha512-pFYqmTw68LXVjeWJMST4+borgQP2AyMNbg1BpZh9LbyhUeNkeaPF9gzfPGUAnSMV3qPYdWUwDIjjCLiSDOl7vg==",
+      "dev": true,
+      "license": "ISC",
+      "dependencies": {
+        "@istanbuljs/schema": "^0.1.2",
+        "glob": "^10.4.1",
+        "minimatch": "^9.0.4"
+      },
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/test-exclude/node_modules/brace-expansion": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
+      "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "balanced-match": "^1.0.0"
+      }
+    },
+    "node_modules/test-exclude/node_modules/minimatch": {
+      "version": "9.0.5",
+      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.5.tgz",
+      "integrity": "sha512-G6T0ZX48xgozx7587koeX9Ys2NYy6Gmv//P89sEte9V9whIapMNF4idKxnW2QtCcLiTWlb/wfCabAtAFWhhBow==",
+      "dev": true,
+      "license": "ISC",
+      "dependencies": {
+        "brace-expansion": "^2.0.1"
+      },
+      "engines": {
+        "node": ">=16 || 14 >=14.17"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
+      }
+    },
     "node_modules/tinybench": {
       "version": "2.9.0",
       "resolved": "https://registry.npmjs.org/tinybench/-/tinybench-2.9.0.tgz",
@@ -4933,9 +5323,9 @@
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-      "resolved": "https://registry.npmjs.org/tinyrainbow/-/tinyrainbow-3.0.3.tgz",
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+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/tinyrainbow/-/tinyrainbow-2.0.0.tgz",
+      "integrity": "sha512-op4nsTR47R6p0vMUUoYl/a+ljLFVtlfaXkLQmqfLR1qHma1h/ysYk4hEXZ880bf2CYgTskvTa/e196Vd5dDQXw==",
       "dev": true,
       "license": "MIT",
       "engines": {
@@ -5309,16 +5699,6 @@
         "url": "https://opencollective.com/vitest"
       }
     },
-    "node_modules/vitest/node_modules/tinyrainbow": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/tinyrainbow/-/tinyrainbow-2.0.0.tgz",
-      "integrity": "sha512-op4nsTR47R6p0vMUUoYl/a+ljLFVtlfaXkLQmqfLR1qHma1h/ysYk4hEXZ880bf2CYgTskvTa/e196Vd5dDQXw==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=14.0.0"
-      }
-    },
     "node_modules/w3c-xmlserializer": {
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/w3c-xmlserializer/-/w3c-xmlserializer-5.0.0.tgz",
@@ -5423,6 +5803,91 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/wrap-ansi": {
+      "version": "8.1.0",
+      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-8.1.0.tgz",
+      "integrity": "sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "ansi-styles": "^6.1.0",
+        "string-width": "^5.0.1",
+        "strip-ansi": "^7.0.1"
+      },
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
+      }
+    },
+    "node_modules/wrap-ansi-cjs": {
+      "name": "wrap-ansi",
+      "version": "7.0.0",
+      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
+      "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "ansi-styles": "^4.0.0",
+        "string-width": "^4.1.0",
+        "strip-ansi": "^6.0.0"
+      },
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
+      }
+    },
+    "node_modules/wrap-ansi-cjs/node_modules/emoji-regex": {
+      "version": "8.0.0",
+      "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
+      "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==",
+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/wrap-ansi-cjs/node_modules/string-width": {
+      "version": "4.2.3",
+      "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
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+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "emoji-regex": "^8.0.0",
+        "is-fullwidth-code-point": "^3.0.0",
+        "strip-ansi": "^6.0.1"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
+    "node_modules/wrap-ansi-cjs/node_modules/strip-ansi": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
+      "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "ansi-regex": "^5.0.1"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
+    "node_modules/wrap-ansi/node_modules/ansi-styles": {
+      "version": "6.2.3",
+      "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.3.tgz",
+      "integrity": "sha512-4Dj6M28JB+oAH8kFkTLUo+a2jwOFkuqb3yucU0CANcRRUbxS0cP0nZYCGjcc3BNXwRIsUVmDGgzawme7zvJHvg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/ansi-styles?sponsor=1"
+      }
+    },
     "node_modules/ws": {
       "version": "8.19.0",
       "resolved": "https://registry.npmjs.org/ws/-/ws-8.19.0.tgz",
diff --git a/frontend/package.json b/frontend/package.json
index ec763b6..44356f3 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -25,6 +25,7 @@
   "devDependencies": {
     "@eslint/js": "^9.39.1",
     "@tailwindcss/vite": "^4.1.18",
+    "@testing-library/dom": "^10.4.0",
     "@testing-library/jest-dom": "^6.9.1",
     "@testing-library/react": "^16.3.2",
     "@testing-library/user-event": "^14.6.1",
@@ -32,7 +33,7 @@
     "@types/react": "^19.2.7",
     "@types/react-dom": "^19.2.3",
     "@vitejs/plugin-react": "^5.1.1",
-    "@vitest/coverage-v8": "^4.0.18",
+    "@vitest/coverage-v8": "^3.2.4",
     "eslint": "^9.39.1",
     "eslint-plugin-react-hooks": "^7.0.1",
     "eslint-plugin-react-refresh": "^0.4.24",

From 199a3855fcad6a0ae1da87b7b8bc7c375faffa11 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 09:27:27 -0700
Subject: [PATCH 100/173] Frontend: Ignore _* unused variables

---
 frontend/eslint.config.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/frontend/eslint.config.js b/frontend/eslint.config.js
index 5e6b472..427b247 100644
--- a/frontend/eslint.config.js
+++ b/frontend/eslint.config.js
@@ -19,5 +19,8 @@ export default defineConfig([
       ecmaVersion: 2020,
       globals: globals.browser,
     },
+    rules: {
+      '@typescript-eslint/no-unused-vars': ['error', { argsIgnorePattern: '^_' }],
+    },
   },
 ])

From b8409c77da8b899cb29f398b599ee29b3acaa42d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:00:01 -0700
Subject: [PATCH 101/173] Delete: Add folder/file exclusion

---
 app/routes/delete.py           | 10 +++++++++-
 app/services/delete_manager.py | 23 ++++++++++++++++++++++-
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/app/routes/delete.py b/app/routes/delete.py
index 2f34db7..b392c03 100644
--- a/app/routes/delete.py
+++ b/app/routes/delete.py
@@ -56,11 +56,19 @@ def scan_folder() -> tuple[Response, int]:
     if not folder_path.is_dir():
         return jsonify({"error": f"Path is not a directory: {folder_path}"}), 400
 
+    excluded_subfolders: list[str] = data.get("excluded_subfolders", [])
+    excluded_files: list[str] = data.get("excluded_files", [])
+
     settings = get_settings()
     manager = get_delete_manager()
 
     try:
-        job = manager.scan_folder(str(folder_path.absolute()), settings.s3_bucket)
+        job = manager.scan_folder(
+            str(folder_path.absolute()),
+            settings.s3_bucket,
+            excluded_subfolders=excluded_subfolders,
+            excluded_files=excluded_files,
+        )
     except PermissionError as e:
         return jsonify({"error": f"Permission denied: {e}"}), 403
 
diff --git a/app/services/delete_manager.py b/app/services/delete_manager.py
index 671909e..a80fafe 100644
--- a/app/services/delete_manager.py
+++ b/app/services/delete_manager.py
@@ -168,12 +168,20 @@ class DeleteManager:
     def __init__(self) -> None:
         self.jobs: dict[str, DeleteJob] = {}
 
-    def scan_folder(self, folder_path: str, bucket: str) -> DeleteJob:
+    def scan_folder(
+        self,
+        folder_path: str,
+        bucket: str,
+        excluded_subfolders: list[str] | None = None,
+        excluded_files: list[str] | None = None,
+    ) -> DeleteJob:
         """Scan a folder for .mcap files and cross-reference with upload cache.
 
         Args:
             folder_path: Local directory to scan
             bucket: S3 bucket to check against
+            excluded_subfolders: Subfolder names to skip
+            excluded_files: Root-level filenames to skip
 
         Returns:
             A new DeleteJob with files matched against the cache
@@ -182,11 +190,24 @@ def scan_folder(self, folder_path: str, bucket: str) -> DeleteJob:
         job = DeleteJob(job_id=job_id)
         cache = get_cache_service()
         folder = Path(folder_path)
+        excluded_subs_set = set(excluded_subfolders or [])
+        excluded_files_set = set(excluded_files or [])
 
         for mcap_path in sorted(folder.rglob("*.mcap")):
             if not mcap_path.is_file():
                 continue
 
+            rel = mcap_path.relative_to(folder)
+            parts = rel.parts
+
+            # Skip root-level files that are excluded
+            if len(parts) == 1 and parts[0] in excluded_files_set:
+                continue
+
+            # Skip files under excluded subfolders
+            if len(parts) > 1 and parts[0] in excluded_subs_set:
+                continue
+
             stat = mcap_path.stat()
             file_size = stat.st_size
             filename = mcap_path.name

From 34558c64f1b9fc8e52c9f06c1cee57a8ece85f62 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:00:27 -0700
Subject: [PATCH 102/173] Frontent: Wrap refs in use effect

---
 frontend/src/hooks/useSSE.ts | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/frontend/src/hooks/useSSE.ts b/frontend/src/hooks/useSSE.ts
index 3bf7c02..cce1988 100644
--- a/frontend/src/hooks/useSSE.ts
+++ b/frontend/src/hooks/useSSE.ts
@@ -21,8 +21,11 @@ export function useSSE({ url, onMessage, onError }: UseSSEOptions): void {
   // because the caller created a new closure.
   const onMessageRef = useRef(onMessage);
   const onErrorRef = useRef(onError);
-  onMessageRef.current = onMessage;
-  onErrorRef.current = onError;
+
+  useEffect(() => {
+    onMessageRef.current = onMessage;
+    onErrorRef.current = onError;
+  });
 
   useEffect(() => {
     if (!url) return;

From 964eec8a2d5a40d4bbc323e60aacf5900f7a8e3e Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:01:22 -0700
Subject: [PATCH 103/173] Frontend: Add is cancelling state to upload

---
 frontend/src/hooks/useUploadJob.ts | 54 +++++++++++++++++++-----------
 1 file changed, 34 insertions(+), 20 deletions(-)

diff --git a/frontend/src/hooks/useUploadJob.ts b/frontend/src/hooks/useUploadJob.ts
index 4429fb6..f11e71c 100644
--- a/frontend/src/hooks/useUploadJob.ts
+++ b/frontend/src/hooks/useUploadJob.ts
@@ -7,7 +7,7 @@
  * only in the terminal event and is stored in uploadStore.completedJob.
  */
 
-import { useCallback, useMemo, useRef, useState } from "react";
+import { useCallback, useEffect, useMemo, useRef, useState } from "react";
 
 import { apiPost } from "../api/client.ts";
 import { useUploadStore } from "../stores/uploadStore.ts";
@@ -27,6 +27,13 @@ interface StatusCounts {
   failed: number;
 }
 
+interface UseUploadJobOptions {
+  /** Called for each file update during analysis/upload. */
+  onFileUpdate?: (file: FileUploadState) => void;
+  /** Called with the full file list on completion. */
+  onCompletion?: (files: FileUploadState[]) => void;
+}
+
 interface UseUploadJobResult {
   startUpload: (
     filePaths: string[],
@@ -40,12 +47,9 @@ interface UseUploadJobResult {
   progressPercent: number;
   eta: number | null;
   isRunning: boolean;
+  isCancelling: boolean;
   uploadedBytesFormatted: string;
   totalBytesFormatted: string;
-  /** Per-file SSE callback ref — wire to FileStore.updateFile. */
-  onFileUpdate: React.MutableRefObject<((file: FileUploadState) => void) | null>;
-  /** Completion callback ref — wire to FileStore.mergeCompletion. */
-  onCompletion: React.MutableRefObject<((files: FileUploadState[]) => void) | null>;
 }
 
 type SSEEvent =
@@ -65,7 +69,7 @@ function isFullJobDict(data: Record<string, unknown>): data is UploadJob & Recor
   return "job_id" in data && "total_bytes" in data && !("type" in data);
 }
 
-export function useUploadJob(): UseUploadJobResult {
+export function useUploadJob(options: UseUploadJobOptions = {}): UseUploadJobResult {
   const [jobId, setJobId] = useState<string | null>(null);
   const [isRunning, setIsRunning] = useState(false);
   const [filesProcessed, setFilesProcessed] = useState(0);
@@ -80,12 +84,18 @@ export function useUploadJob(): UseUploadJobResult {
   const [eta, setEta] = useState<number | null>(null);
   const [uploadedBytesFormatted, setUploadedBytesFormatted] = useState("");
   const [totalBytesFormatted, setTotalBytesFormatted] = useState("");
+  const [isCancelling, setIsCancelling] = useState(false);
 
   const { setUploadJobId, setCompletedJob } = useUploadStore();
 
-  // Callback refs for per-file updates — wired by UploadPage to FileStore
-  const onFileUpdateRef = useRef<((file: FileUploadState) => void) | null>(null);
-  const onCompletionRef = useRef<((files: FileUploadState[]) => void) | null>(null);
+  // Callback refs — kept in sync with latest options via effect
+  const onFileUpdateRef = useRef(options.onFileUpdate);
+  const onCompletionRef = useRef(options.onCompletion);
+
+  useEffect(() => {
+    onFileUpdateRef.current = options.onFileUpdate;
+    onCompletionRef.current = options.onCompletion;
+  });
 
   /** Handle each SSE event. */
   const handleMessage = useCallback(
@@ -172,6 +182,7 @@ export function useUploadJob(): UseUploadJobResult {
           p.status === "cancelled"
         ) {
           setIsRunning(false);
+          setIsCancelling(false);
           setJobId(null);
         }
         return;
@@ -196,6 +207,7 @@ export function useUploadJob(): UseUploadJobResult {
         // Notify unified table with all completion data
         onCompletionRef.current?.(job.files);
         setIsRunning(false);
+        setIsCancelling(false);
         setJobId(null);
         return;
       }
@@ -215,6 +227,7 @@ export function useUploadJob(): UseUploadJobResult {
       // Stream closed — if we're still "running" the server ended it.
       if (isRunning) {
         setIsRunning(false);
+        setIsCancelling(false);
         setJobId(null);
       }
     },
@@ -232,6 +245,7 @@ export function useUploadJob(): UseUploadJobResult {
       setEta(null);
       setUploadedBytesFormatted("");
       setTotalBytesFormatted("");
+      setIsCancelling(false);
       setIsRunning(true);
 
       try {
@@ -253,18 +267,19 @@ export function useUploadJob(): UseUploadJobResult {
     [setUploadJobId],
   );
 
-  /** Cancel the current upload job. */
+  /** Cancel the current upload job. SSE terminal event handles cleanup. */
   const cancelUpload = useCallback(async () => {
     const currentJobId = useUploadStore.getState().uploadJobId;
-    if (currentJobId) {
-      try {
-        await apiPost(`/api/upload/cancel/${currentJobId}`);
-      } catch {
-        // Ignore
-      }
+    if (!currentJobId) return;
+    setIsCancelling(true);
+    try {
+      await apiPost(`/api/upload/cancel/${currentJobId}`);
+    } catch {
+      // If the cancel request itself fails, force-close
+      setIsRunning(false);
+      setJobId(null);
+      setIsCancelling(false);
     }
-    setIsRunning(false);
-    setJobId(null);
   }, []);
 
   return {
@@ -277,9 +292,8 @@ export function useUploadJob(): UseUploadJobResult {
     progressPercent,
     eta,
     isRunning,
+    isCancelling,
     uploadedBytesFormatted,
     totalBytesFormatted,
-    onFileUpdate: onFileUpdateRef,
-    onCompletion: onCompletionRef,
   };
 }

From d8a52f010a94e719c161242323165ed5f2e4cb21 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:01:56 -0700
Subject: [PATCH 104/173] Frontend: Add exclusions to delete scan

---
 frontend/src/hooks/useDeleteScan.ts | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/frontend/src/hooks/useDeleteScan.ts b/frontend/src/hooks/useDeleteScan.ts
index cecdcd6..1bde0c9 100644
--- a/frontend/src/hooks/useDeleteScan.ts
+++ b/frontend/src/hooks/useDeleteScan.ts
@@ -11,8 +11,13 @@ import { apiPost } from "../api/client.ts";
 import { useDeleteStore } from "../stores/deleteStore.ts";
 import type { DeleteScanResponse } from "../types/delete.ts";
 
+interface ScanExclusions {
+  subfolders: string[];
+  files: string[];
+}
+
 interface UseDeleteScanResult {
-  scan: (folderPath: string) => Promise<void>;
+  scan: (folderPath: string, exclusions?: ScanExclusions) => Promise<void>;
   isScanning: boolean;
 }
 
@@ -21,12 +26,15 @@ export function useDeleteScan(): UseDeleteScanResult {
     useDeleteStore();
 
   const scan = useCallback(
-    async (folderPath: string) => {
+    async (folderPath: string, exclusions?: ScanExclusions) => {
       setIsScanning(true);
       try {
-        const res = await apiPost<DeleteScanResponse>("/api/delete/scan", {
-          folder_path: folderPath,
-        });
+        const body: Record<string, unknown> = { folder_path: folderPath };
+        if (exclusions) {
+          body.excluded_subfolders = exclusions.subfolders;
+          body.excluded_files = exclusions.files;
+        }
+        const res = await apiPost<DeleteScanResponse>("/api/delete/scan", body);
         setDeleteJobId(res.job_id);
         setScanResults(res.files, res.total_size);
       } finally {

From 84c19d31c44ee27f2092bf3a250d8b3b46198e2b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:02:23 -0700
Subject: [PATCH 105/173] Frontend: Add isCancelling state to delete page

---
 frontend/src/pages/DeletePage.tsx | 66 +++++++++++++++++++++++++------
 1 file changed, 54 insertions(+), 12 deletions(-)

diff --git a/frontend/src/pages/DeletePage.tsx b/frontend/src/pages/DeletePage.tsx
index 56017e5..782dbf1 100644
--- a/frontend/src/pages/DeletePage.tsx
+++ b/frontend/src/pages/DeletePage.tsx
@@ -11,10 +11,13 @@
 import { useCallback, useEffect, useMemo, useState } from "react";
 
 import ProgressBar from "../components/common/ProgressBar.tsx";
+import Spinner from "../components/common/Spinner.tsx";
 import StatCard from "../components/common/StatCard.tsx";
 import DeleteConfirmation from "../components/delete/DeleteConfirmation.tsx";
 import DeleteStepper from "../components/delete/DeleteStepper.tsx";
+import CancelConfirmModal from "../components/upload/CancelConfirmModal.tsx";
 import FolderBrowser from "../components/upload/FolderBrowser.tsx";
+import type { FolderExclusions } from "../components/upload/FolderBrowser.tsx";
 import { useDeleteJob } from "../hooks/useDeleteJob.ts";
 import { useDeleteScan } from "../hooks/useDeleteScan.ts";
 import { useAppStore } from "../stores/appStore.ts";
@@ -73,14 +76,16 @@ export default function DeletePage() {
   // Pagination for file table
   const [page, setPage] = useState(0);
   const pageSize = 50;
+  const [showCancelModal, setShowCancelModal] = useState(false);
+  const [refreshKey, setRefreshKey] = useState(0);
 
   // ── Step transitions ──
 
   const handleFolderSelected = useCallback(
-    async (path: string) => {
+    async (path: string, exclusions?: FolderExclusions) => {
       setFolderPath(path);
       setStep(2);
-      await scan(path);
+      await scan(path, exclusions);
     },
     [setFolderPath, setStep, scan],
   );
@@ -90,6 +95,15 @@ export default function DeletePage() {
     await deleteJob.startDelete();
   }, [setStep, deleteJob]);
 
+  const handleCancelClick = useCallback(() => {
+    setShowCancelModal(true);
+  }, []);
+
+  const handleConfirmCancel = useCallback(async () => {
+    setShowCancelModal(false);
+    await deleteJob.cancelDelete();
+  }, [deleteJob]);
+
   // Auto-advance from Step 4 to Step 5 when deletion completes
   useEffect(() => {
     if (step === 4 && !deleteJob.isRunning && completedJob) {
@@ -98,8 +112,13 @@ export default function DeletePage() {
   }, [step, deleteJob.isRunning, completedJob, setStep]);
 
   const handleStartOver = useCallback(() => {
+    const previousPath = folderPath;
     reset();
-  }, [reset]);
+    // Preserve the folder path so the browser reopens at the same location
+    if (previousPath) setFolderPath(previousPath);
+    // Bump key to force FolderBrowser to re-mount with fresh data
+    setRefreshKey((k) => k + 1);
+  }, [reset, folderPath, setFolderPath]);
 
   const handleBack = useCallback(() => {
     if (step === 2) {
@@ -149,6 +168,7 @@ export default function DeletePage() {
       {/* Step 1: Folder Selection */}
       {step === 1 && (
         <FolderBrowser
+          key={refreshKey}
           onFolderSelected={handleFolderSelected}
           initialPath={folderPath || defaultUploadFolder || undefined}
           mode="delete"
@@ -196,7 +216,7 @@ export default function DeletePage() {
                         Size
                       </th>
                       <th className="text-left px-4 py-2 font-medium text-gray-600">
-                        S3 Path
+                        Cloud Path
                       </th>
                     </tr>
                   </thead>
@@ -311,20 +331,42 @@ export default function DeletePage() {
             percent={progressPercent}
             label={
               deleteJob.jobStatus === "verifying"
-                ? "Verifying files against S3..."
+                ? "Verifying files against cloud storage..."
                 : deleteJob.jobStatus === "deleting"
                   ? "Clearing verified files..."
                   : "Processing..."
             }
           />
 
-          <button
-            type="button"
-            onClick={deleteJob.cancelDelete}
-            className="px-4 py-2 text-sm font-medium text-red-700 bg-red-50 border border-red-200 rounded-md hover:bg-red-100"
-          >
-            Cancel
-          </button>
+          {!deleteJob.isCancelling && (
+            <button
+              type="button"
+              onClick={handleCancelClick}
+              className="px-4 py-2 text-sm font-medium text-red-700 bg-red-50 border border-red-200 rounded-md hover:bg-red-100"
+            >
+              Cancel
+            </button>
+          )}
+
+          {/* Cancel confirmation modal */}
+          <CancelConfirmModal
+            isOpen={showCancelModal}
+            onClose={() => setShowCancelModal(false)}
+            onConfirm={handleConfirmCancel}
+            filesProcessed={deleteJob.filesProcessed}
+            totalFiles={deleteJob.totalFiles}
+          />
+
+          {/* Cancelling overlay */}
+          {deleteJob.isCancelling && (
+            <div className="fixed inset-0 z-50 flex items-center justify-center bg-gray-900/40 backdrop-blur-sm">
+              <div className="bg-white rounded-lg shadow-xl px-8 py-6 flex flex-col items-center gap-3">
+                <Spinner />
+                <p className="text-sm font-medium text-gray-700">Cancelling...</p>
+                <p className="text-xs text-gray-500">Waiting for in-progress operations to finish.</p>
+              </div>
+            </div>
+          )}
         </div>
       )}
 

From 4745eceae4b3618f99ae6ee1fbd379090ee6f6d7 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:02:43 -0700
Subject: [PATCH 106/173] Frontend: Add Cancel Confirmation modal

---
 .../components/upload/CancelConfirmModal.tsx  | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 frontend/src/components/upload/CancelConfirmModal.tsx

diff --git a/frontend/src/components/upload/CancelConfirmModal.tsx b/frontend/src/components/upload/CancelConfirmModal.tsx
new file mode 100644
index 0000000..253149c
--- /dev/null
+++ b/frontend/src/components/upload/CancelConfirmModal.tsx
@@ -0,0 +1,66 @@
+/**
+ * Confirmation modal shown when the user clicks "Cancel Upload".
+ */
+
+import Modal from "../common/Modal.tsx";
+import { WarningIcon } from "../../utils/icons.tsx";
+
+interface CancelConfirmModalProps {
+  isOpen: boolean;
+  onClose: () => void;
+  onConfirm: () => void;
+  filesProcessed: number;
+  totalFiles: number;
+}
+
+export default function CancelConfirmModal({
+  isOpen,
+  onClose,
+  onConfirm,
+  filesProcessed,
+  totalFiles,
+}: CancelConfirmModalProps) {
+  const remaining = totalFiles - filesProcessed;
+
+  return (
+    <Modal
+      isOpen={isOpen}
+      onClose={onClose}
+      title="Cancel Upload?"
+      footer={
+        <div className="flex gap-3">
+          <button
+            type="button"
+            onClick={onClose}
+            className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
+          >
+            Keep Uploading
+          </button>
+          <button
+            type="button"
+            onClick={onConfirm}
+            className="px-4 py-2 text-sm font-medium rounded transition-colors bg-red-600 text-white hover:bg-red-700"
+          >
+            Cancel Upload
+          </button>
+        </div>
+      }
+    >
+      <div className="space-y-3">
+        <div className="flex items-start gap-3 p-3 bg-amber-50 rounded-lg border border-amber-200">
+          <WarningIcon className="w-5 h-5 text-amber-600 flex-shrink-0 mt-0.5" />
+          <div className="text-sm text-amber-800">
+            <p>
+              <strong>{filesProcessed}</strong> of <strong>{totalFiles}</strong> files
+              have been processed so far. Cancelling will stop the remaining{" "}
+              <strong>{remaining}</strong> file{remaining !== 1 ? "s" : ""} from being uploaded.
+            </p>
+            <p className="mt-2 text-amber-700">
+              Files already uploaded will remain in cloud storage.
+            </p>
+          </div>
+        </div>
+      </div>
+    </Modal>
+  );
+}

From 4ec3d5b9921b1c97628d4c9e5e48fd4567f8c1ac Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:04:02 -0700
Subject: [PATCH 107/173] Frontend: Add is cancelling state to upload

---
 frontend/src/pages/UploadPage.tsx | 111 ++++++++++++++++++++----------
 1 file changed, 76 insertions(+), 35 deletions(-)

diff --git a/frontend/src/pages/UploadPage.tsx b/frontend/src/pages/UploadPage.tsx
index 146c136..6f27c7d 100644
--- a/frontend/src/pages/UploadPage.tsx
+++ b/frontend/src/pages/UploadPage.tsx
@@ -6,8 +6,10 @@
  *   with phase-aware header, toolbar, and footer.
  */
 
-import { useCallback, useEffect, useLayoutEffect, useMemo, useState } from "react";
+import { useCallback, useEffect, useMemo, useRef, useState } from "react";
 
+import Spinner from "../components/common/Spinner.tsx";
+import CancelConfirmModal from "../components/upload/CancelConfirmModal.tsx";
 import ConfirmModal from "../components/upload/ConfirmModal.tsx";
 import FolderBrowser from "../components/upload/FolderBrowser.tsx";
 import type { FolderExclusions } from "../components/upload/FolderBrowser.tsx";
@@ -48,48 +50,53 @@ export default function UploadPage() {
     totals,
   } = useFolderScan();
 
-  const uploadJob = useUploadJob();
-
   // Unified file store
   const { files, store } = useFileStore();
 
+  // SSE callback: map each file event to the FileStore
+  const handleFileUpdate = useCallback((file: FileUploadState) => {
+    const statusMap: Record<string, "in_progress" | "completed" | "skipped" | "failed" | "queued"> = {
+      analyzing: "in_progress",
+      uploading: "in_progress",
+      completed: "completed",
+      skipped: "skipped",
+      failed: "failed",
+      cancelled: "failed",
+    };
+    store.updateFile(file.local_path, {
+      status: statusMap[file.status] ?? "queued",
+      progressPercent: file.progress_percent,
+      s3Path: file.s3_path || undefined,
+      error: file.error_message || undefined,
+      duration: file.upload_duration_seconds,
+      speed: file.upload_speed_mbps,
+    });
+  }, [store]);
+
+  // SSE callback: merge full completion data into the FileStore
+  const handleCompletion = useCallback((completionFiles: FileUploadState[]) => {
+    store.mergeCompletion(completionFiles);
+  }, [store]);
+
+  const uploadJob = useUploadJob({
+    onFileUpdate: handleFileUpdate,
+    onCompletion: handleCompletion,
+  });
+
   // Local state
   const [showConfirmModal, setShowConfirmModal] = useState(false);
+  const [showCancelModal, setShowCancelModal] = useState(false);
   const [pendingSelectedPaths, setPendingSelectedPaths] = useState<string[]>([]);
   const [selectedPaths, setSelectedPaths] = useState<Set<string>>(new Set());
 
   // Derive phase from step
   const phase: UploadPhase = step <= 2 ? "review" : step === 3 ? "uploading" : "summary";
 
-  // ── Wire SSE callbacks to FileStore (useLayoutEffect to avoid race) ──
-
-  useLayoutEffect(() => {
-    uploadJob.onFileUpdate.current = (file: FileUploadState) => {
-      const statusMap: Record<string, "in_progress" | "completed" | "skipped" | "failed" | "queued"> = {
-        analyzing: "in_progress",
-        uploading: "in_progress",
-        completed: "completed",
-        skipped: "skipped",
-        failed: "failed",
-        cancelled: "failed",
-      };
-      store.updateFile(file.local_path, {
-        status: statusMap[file.status] ?? "queued",
-        progressPercent: file.progress_percent,
-        s3Path: file.s3_path || undefined,
-        error: file.error_message || undefined,
-        duration: file.upload_duration_seconds,
-        speed: file.upload_speed_mbps,
-      });
-    };
-    uploadJob.onCompletion.current = (completionFiles: FileUploadState[]) => {
-      store.mergeCompletion(completionFiles);
-    };
-  });
-
   // ── Sync FileStore from scan data as folders arrive ──
 
-  useEffect(() => {
+  const prevFoldersRef = useRef(folders);
+  if (folders !== prevFoldersRef.current) {
+    prevFoldersRef.current = folders;
     if (folders.length > 0 && step >= 2) {
       store.buildFromScan(folders);
       // Auto-select new files
@@ -103,7 +110,7 @@ export default function UploadPage() {
       }
       setSelectedPaths(newSelected);
     }
-  }, [folders, step, store]);
+  }
 
   // ── Freeze/unfreeze sort on phase transitions ──
 
@@ -149,7 +156,18 @@ export default function UploadPage() {
     [pendingSelectedPaths, setStep, uploadJob, store],
   );
 
-  /** Step 3 -> 4: Upload finished, advance to completion. */
+  /** Cancel button → show confirmation modal. */
+  const handleCancelClick = useCallback(() => {
+    setShowCancelModal(true);
+  }, []);
+
+  /** Cancel confirmed → send cancel to backend, overlay locks the screen. */
+  const handleConfirmCancel = useCallback(async () => {
+    setShowCancelModal(false);
+    await uploadJob.cancelUpload();
+  }, [uploadJob]);
+
+  /** Step 3 -> 4: Upload finished (or cancelled), advance to completion. */
   useEffect(() => {
     if (step === 3 && !uploadJob.isRunning && completedJob) {
       setStep(4);
@@ -194,7 +212,10 @@ export default function UploadPage() {
     });
   }, []);
 
-  const allFiles = useMemo(() => Array.from(store.getAllRows().values()), [files]);
+  // `files` is listed as a dep to re-derive when the store snapshot changes
+  // (store itself is a stable singleton).
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  const allFiles = useMemo(() => Array.from(store.getAllRows().values()), [store, files]);
 
   const toggleAllFiltered = useCallback(() => {
     const filteredPaths = files.map((f) => f.path);
@@ -371,8 +392,8 @@ export default function UploadPage() {
             onBack={handleBack}
             onStartUpload={handleStartUploadClick}
             selectedNewCount={selectedNewCount}
-            onCancel={uploadJob.cancelUpload}
-            isRunning={uploadJob.isRunning}
+            onCancel={handleCancelClick}
+            isRunning={uploadJob.isRunning && !uploadJob.isCancelling}
             onDownloadCsv={handleDownloadCsv}
             onUploadMore={handleUploadMore}
             failedCount={uploadJob.statusCounts.failed}
@@ -389,6 +410,26 @@ export default function UploadPage() {
               totalSize={selectedTotals.totalSize}
             />
           )}
+
+          {/* Cancel confirmation modal */}
+          <CancelConfirmModal
+            isOpen={showCancelModal}
+            onClose={() => setShowCancelModal(false)}
+            onConfirm={handleConfirmCancel}
+            filesProcessed={uploadJob.filesProcessed}
+            totalFiles={uploadJob.totalFiles}
+          />
+
+          {/* Cancelling overlay — locks the screen while backend winds down */}
+          {uploadJob.isCancelling && (
+            <div className="fixed inset-0 z-50 flex items-center justify-center bg-gray-900/40 backdrop-blur-sm">
+              <div className="bg-white rounded-lg shadow-xl px-8 py-6 flex flex-col items-center gap-3">
+                <Spinner />
+                <p className="text-sm font-medium text-gray-700">Cancelling upload...</p>
+                <p className="text-xs text-gray-500">Waiting for in-progress files to finish.</p>
+              </div>
+            </div>
+          )}
         </div>
       )}
     </div>

From 174448f0e8724e0552a6cb0f676645405e5b86bf Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:04:37 -0700
Subject: [PATCH 108/173] Frontend: Add refresh button to FolderBrowser

---
 .../src/components/upload/FolderBrowser.tsx   | 51 +++++++++++++++++--
 1 file changed, 47 insertions(+), 4 deletions(-)

diff --git a/frontend/src/components/upload/FolderBrowser.tsx b/frontend/src/components/upload/FolderBrowser.tsx
index 79b770d..51b9876 100644
--- a/frontend/src/components/upload/FolderBrowser.tsx
+++ b/frontend/src/components/upload/FolderBrowser.tsx
@@ -23,6 +23,7 @@ import {
   ChevronRightIcon,
   CheckIcon,
   PlusIcon,
+  RefreshIcon,
   UploadIcon,
 } from "../../utils/icons.tsx";
 
@@ -124,6 +125,15 @@ export default function FolderBrowser({
     navigate(initialPath);
   }, [navigate, initialPath]);
 
+  /** Re-fetch the current directory without resetting to initialPath. */
+  const refresh = useCallback(() => {
+    if (data) {
+      navigate(data.current_path);
+    } else {
+      navigate(initialPath);
+    }
+  }, [data, navigate, initialPath]);
+
   // Reset checked state and search when data changes (new directory loaded)
   useEffect(() => {
     if (!data) return;
@@ -151,6 +161,30 @@ export default function FolderBrowser({
   const checkedCount = checkedFolders.size + checkedFiles.size;
   const allChecked = totalItems > 0 && checkedCount === totalItems;
 
+  // Count actionable files among the user's current selection
+  const selectedActionableCount = useMemo(() => {
+    if (!data) return 0;
+    let count = 0;
+    // Checked folders: sum their actionable file counts
+    for (const folder of data.folders) {
+      if (checkedFolders.has(folder.name)) {
+        count += mode === "upload"
+          ? folder.mcap_count - folder.already_uploaded
+          : folder.already_uploaded;
+      }
+    }
+    // Checked loose files: count actionable ones
+    for (const file of data.files) {
+      if (checkedFiles.has(file.name)) {
+        const isUploaded = file.already_uploaded ?? false;
+        if (mode === "upload" ? !isUploaded : isUploaded) {
+          count += 1;
+        }
+      }
+    }
+    return count;
+  }, [data, checkedFolders, checkedFiles, mode]);
+
   const selectAll = useCallback(() => {
     if (!data) return;
     setCheckedFolders(new Set(data.folders.map((f) => f.name)));
@@ -306,9 +340,18 @@ export default function FolderBrowser({
 
         {/* Main content area */}
         <div className="flex-1 flex flex-col min-w-0">
-          {/* Breadcrumbs */}
-          <div className="px-4 py-2 border-b border-gray-100 bg-gray-50/50">
+          {/* Breadcrumbs + refresh */}
+          <div className="px-4 py-2 border-b border-gray-100 bg-gray-50/50 flex items-center justify-between">
             <Breadcrumb items={breadcrumbItems} />
+            <button
+              type="button"
+              onClick={refresh}
+              disabled={loading}
+              title="Refresh folder"
+              className="p-1 text-gray-400 hover:text-gray-600 rounded hover:bg-gray-200 transition-colors disabled:opacity-50"
+            >
+              <RefreshIcon className={`w-3.5 h-3.5 ${loading ? "animate-spin" : ""}`} />
+            </button>
           </div>
 
           {/* Summary bar — always visible when we have data and MCAP files exist */}
@@ -359,7 +402,7 @@ export default function FolderBrowser({
                     ${cfg.buttonColor}
                     disabled:bg-gray-300 disabled:text-gray-500 disabled:cursor-not-allowed`}
                 >
-                  {cfg.buttonLabel(actionableCount)}
+                  {cfg.buttonLabel(selectedActionableCount)}
                   <ChevronRightIcon className="w-4 h-4 ml-1 inline-block" />
                 </button>
               </div>
@@ -581,7 +624,7 @@ function FolderList({
                 {/* Upload status indicator */}
                 {allUploaded && (
                   <span className="inline-flex items-center gap-1 text-xs text-gray-500">
-                    <CheckIcon className="w-3.5 h-3.5 text-green-500" />
+                    <CheckIcon className="w-3.5 h-3.5 text-green-700" />
                     {folder.mcap_count}/{folder.mcap_count} uploaded
                   </span>
                 )}

From 377259290c0ce932da2eb7224217653e08be0f77 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:05:03 -0700
Subject: [PATCH 109/173] Frontend: Add more context to uploaded success
 messages

---
 .../src/components/upload/UploadFooter.tsx    | 44 +++++++++++--------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/frontend/src/components/upload/UploadFooter.tsx b/frontend/src/components/upload/UploadFooter.tsx
index d39c786..fe60a94 100644
--- a/frontend/src/components/upload/UploadFooter.tsx
+++ b/frontend/src/components/upload/UploadFooter.tsx
@@ -3,9 +3,10 @@
  *
  * - Review: Back + Start Upload
  * - Upload: Cancel Upload
- * - Summary: Download CSV + Upload More
+ * - Summary: info blurb + Download CSV + Upload More
  */
 
+import { Link } from "react-router-dom";
 import type { UploadPhase } from "../../types/upload.ts";
 import { ChevronRightIcon, XCircleIcon, DownloadIcon, UploadIcon } from "../../utils/icons.tsx";
 
@@ -81,23 +82,30 @@ export default function UploadFooter({
 
   // Summary
   return (
-    <div className="flex items-center justify-center gap-4 pt-2">
-      <button
-        type="button"
-        onClick={onDownloadCsv}
-        className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
-      >
-        <DownloadIcon className="w-4 h-4 mr-1 inline-block" />
-        Download CSV
-      </button>
-      <button
-        type="button"
-        onClick={onUploadMore}
-        className="px-6 py-2 text-sm font-medium rounded transition-colors bg-nlr-blue text-white hover:bg-blue-700"
-      >
-        <UploadIcon className="w-4 h-4 mr-1 inline-block" />
-        Upload More
-      </button>
+    <div className="space-y-3 pt-2">
+      <p className="text-xs text-gray-500 text-center">
+        These results have been saved and can be reviewed anytime on the{" "}
+        <Link to="/logs" className="text-nlr-blue hover:underline font-medium">History</Link> page.
+      </p>
+      <div className="flex items-center justify-center gap-4">
+        <button
+          type="button"
+          onClick={onDownloadCsv}
+          title="Export a spreadsheet of all files and their upload status"
+          className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
+        >
+          <DownloadIcon className="w-4 h-4 mr-1 inline-block" />
+          Export Summary CSV
+        </button>
+        <button
+          type="button"
+          onClick={onUploadMore}
+          className="px-6 py-2 text-sm font-medium rounded transition-colors bg-nlr-blue text-white hover:bg-blue-700"
+        >
+          <UploadIcon className="w-4 h-4 mr-1 inline-block" />
+          Upload More
+        </button>
+      </div>
     </div>
   );
 }

From e5f133c5ce58a3a20603ee7c429c7750986b1fca Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:05:42 -0700
Subject: [PATCH 110/173] Frontend: Ignore useVirtualizer type error

---
 frontend/src/components/upload/UnifiedFileTable.tsx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/frontend/src/components/upload/UnifiedFileTable.tsx b/frontend/src/components/upload/UnifiedFileTable.tsx
index ccf10fb..82485e3 100644
--- a/frontend/src/components/upload/UnifiedFileTable.tsx
+++ b/frontend/src/components/upload/UnifiedFileTable.tsx
@@ -56,6 +56,7 @@ export default function UnifiedFileTable({
 }: UnifiedFileTableProps) {
   const scrollContainerRef = useRef<HTMLDivElement>(null);
 
+  // eslint-disable-next-line react-hooks/incompatible-library
   const rowVirtualizer = useVirtualizer({
     count: files.length,
     getScrollElement: () => scrollContainerRef.current,

From 77b93c63e4fad0cbf0069c960916e35a891e2b6b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:06:06 -0700
Subject: [PATCH 111/173] Frontend: Use darker green for success

---
 frontend/src/components/common/AlertBanner.tsx      |  4 ++--
 frontend/src/components/common/Stepper.tsx          | 10 +++++-----
 frontend/src/components/upload/UnifiedFileTable.tsx |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/frontend/src/components/common/AlertBanner.tsx b/frontend/src/components/common/AlertBanner.tsx
index 9013a4f..5b802c4 100644
--- a/frontend/src/components/common/AlertBanner.tsx
+++ b/frontend/src/components/common/AlertBanner.tsx
@@ -51,8 +51,8 @@ const iconColorStyles: Record<AlertType, string> = {
   info: "text-blue-500",
   warning: "text-yellow-500",
   error: "text-red-500",
-  success: "text-green-500",
-  shield: "text-green-500",
+  success: "text-green-700",
+  shield: "text-green-700",
 };
 
 export default function AlertBanner({
diff --git a/frontend/src/components/common/Stepper.tsx b/frontend/src/components/common/Stepper.tsx
index 7ba4754..0a9b244 100644
--- a/frontend/src/components/common/Stepper.tsx
+++ b/frontend/src/components/common/Stepper.tsx
@@ -56,8 +56,8 @@ export default function Stepper({
         let circleClass =
           "w-9 h-9 rounded-full flex items-center justify-center text-sm font-bold transition-colors";
         if (isDone) {
-          circleClass += " bg-green-500 text-white";
-          if (canClick) circleClass += " cursor-pointer hover:bg-green-600";
+          circleClass += " bg-green-700 text-white";
+          if (canClick) circleClass += " cursor-pointer hover:bg-green-800";
         } else if (isActive) {
           circleClass += " bg-nlr-blue text-white";
         } else {
@@ -79,12 +79,12 @@ export default function Stepper({
                 aria-label={`Step ${step.number}: ${step.label}${isDone ? " (completed)" : ""}${isActive ? " (current)" : ""}`}
                 data-testid={`${testIdPrefix}-${step.number}`}
               >
-                {isDone ? <CheckIcon className="w-5 h-5" /> : step.number}
+                {isDone ? <CheckIcon className="w-5 h-5" data-testid="checkmark-icon" /> : step.number}
               </button>
               <span
                 className={`mt-1.5 text-xs font-medium ${
                   isDone
-                    ? "text-green-600"
+                    ? "text-green-800"
                     : isActive
                       ? "text-nlr-blue"
                       : "text-gray-400"
@@ -96,7 +96,7 @@ export default function Stepper({
             {showConnector && (
               <div
                 className={`w-16 sm:w-24 h-0.5 mx-2 mb-5 ${
-                  step.number < currentStep ? "bg-green-500" : "bg-gray-300"
+                  step.number < currentStep ? "bg-green-700" : "bg-gray-300"
                 }`}
               />
             )}
diff --git a/frontend/src/components/upload/UnifiedFileTable.tsx b/frontend/src/components/upload/UnifiedFileTable.tsx
index 82485e3..9d27915 100644
--- a/frontend/src/components/upload/UnifiedFileTable.tsx
+++ b/frontend/src/components/upload/UnifiedFileTable.tsx
@@ -294,7 +294,7 @@ function StatusIcon({ status }: { status: UnifiedStatus }) {
     case "in_progress":
       return <SpinnerIcon className="w-4 h-4 text-nlr-blue animate-spin" />;
     case "completed":
-      return <CheckIcon className="w-4 h-4 text-green-500" strokeWidth={2.5} />;
+      return <CheckIcon className="w-4 h-4 text-green-700" strokeWidth={2.5} />;
     case "failed":
       return <XIcon className="w-4 h-4 text-red-500" strokeWidth={2.5} />;
     case "skipped":

From 40a2ba81d8c791a50aef9d1de205970d1976b50c Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:07:00 -0700
Subject: [PATCH 112/173] Frontend: Add link to uploaded files in delete screen

---
 .../components/delete/DeleteConfirmation.tsx    | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/frontend/src/components/delete/DeleteConfirmation.tsx b/frontend/src/components/delete/DeleteConfirmation.tsx
index a973ac2..5479c1d 100644
--- a/frontend/src/components/delete/DeleteConfirmation.tsx
+++ b/frontend/src/components/delete/DeleteConfirmation.tsx
@@ -6,6 +6,7 @@
  */
 
 import { useState } from "react";
+import { Link } from "react-router-dom";
 
 import { formatBytes } from "../../utils/format/bytes.ts";
 import AlertBanner from "../common/AlertBanner.tsx";
@@ -43,11 +44,19 @@ export default function DeleteConfirmation({
         }
       />
 
-      {/* S3 reassurance */}
+      {/* Cloud reassurance */}
       <AlertBanner
         type="shield"
-        title="S3 data will NOT be affected"
-        message="Only local copies are deleted. Your files in S3 remain safe and unchanged. Each file is verified against S3 before deletion."
+        title="Cloud storage will NOT be affected"
+        message={
+          <>
+            Only local copies are removed. Your files in{" "}
+            <Link to="/files" className="underline hover:no-underline font-medium" title="Browse uploaded files in cloud storage">
+              cloud storage
+            </Link>
+            {" "}remain safe and unchanged. Each file is verified against the cloud upload before removal.
+          </>
+        }
       />
 
       {/* Type-to-confirm */}
@@ -79,7 +88,7 @@ export default function DeleteConfirmation({
         />
         <span className="text-sm text-gray-700">
           I understand that cleared files cannot be recovered from this drive
-          and that the S3 copies have been verified.
+          and that the cloud uploads have been verified.
         </span>
       </label>
 

From 5723e0bd9cff5dad861923e63771cf5cbf6b6f52 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:07:20 -0700
Subject: [PATCH 113/173] Frontend: Add is delete hooks for cancelling state

---
 frontend/src/hooks/useDeleteJob.ts | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/frontend/src/hooks/useDeleteJob.ts b/frontend/src/hooks/useDeleteJob.ts
index e02823d..49e4a80 100644
--- a/frontend/src/hooks/useDeleteJob.ts
+++ b/frontend/src/hooks/useDeleteJob.ts
@@ -32,6 +32,7 @@ interface UseDeleteJobResult {
   statusCounts: StatusCounts;
   totalDeletedSize: number;
   isRunning: boolean;
+  isCancelling: boolean;
   jobStatus: string;
 }
 
@@ -72,6 +73,7 @@ export function useDeleteJob(): UseDeleteJobResult {
   });
   const [totalDeletedSize, setTotalDeletedSize] = useState(0);
   const [jobStatus, setJobStatus] = useState("pending");
+  const [isCancelling, setIsCancelling] = useState(false);
   const [activeJobId, setActiveJobId] = useState<string | null>(null);
 
   const { deleteJobId, setCompletedJob, setIsDeleting } = useDeleteStore();
@@ -99,6 +101,7 @@ export function useDeleteJob(): UseDeleteJobResult {
         setTotalDeletedSize(c.total_deleted_size);
         setJobStatus(c.status);
         setIsRunning(false);
+        setIsCancelling(false);
         setIsDeleting(false);
         setActiveJobId(null);
         setCompletedJob(c as unknown as DeleteJobResult);
@@ -122,6 +125,7 @@ export function useDeleteJob(): UseDeleteJobResult {
     onError: () => {
       if (isRunning) {
         setIsRunning(false);
+        setIsCancelling(false);
         setIsDeleting(false);
         setActiveJobId(null);
       }
@@ -141,6 +145,7 @@ export function useDeleteJob(): UseDeleteJobResult {
     });
     setTotalDeletedSize(0);
     setJobStatus("verifying");
+    setIsCancelling(false);
     setIsRunning(true);
     setIsDeleting(true);
 
@@ -153,18 +158,20 @@ export function useDeleteJob(): UseDeleteJobResult {
     }
   }, [deleteJobId, setIsDeleting]);
 
+  /** Cancel the delete job. SSE terminal event handles cleanup. */
   const cancelDelete = useCallback(async () => {
     const jobId = useDeleteStore.getState().deleteJobId;
-    if (jobId) {
-      try {
-        await apiPost(`/api/delete/cancel/${jobId}`);
-      } catch {
-        // Ignore
-      }
+    if (!jobId) return;
+    setIsCancelling(true);
+    try {
+      await apiPost(`/api/delete/cancel/${jobId}`);
+    } catch {
+      // If cancel request fails, force-close
+      setIsRunning(false);
+      setIsCancelling(false);
+      setIsDeleting(false);
+      setActiveJobId(null);
     }
-    setIsRunning(false);
-    setIsDeleting(false);
-    setActiveJobId(null);
   }, [setIsDeleting]);
 
   return {
@@ -175,6 +182,7 @@ export function useDeleteJob(): UseDeleteJobResult {
     statusCounts,
     totalDeletedSize,
     isRunning,
+    isCancelling,
     jobStatus,
   };
 }

From 6ff0f9bb99368f68defd9db6e69e9ca47ea24fdb Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:07:42 -0700
Subject: [PATCH 114/173] Frontend: Remove unused icon sizes const

---
 frontend/src/utils/icons.tsx | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
index 6ca0e21..d917a5d 100644
--- a/frontend/src/utils/icons.tsx
+++ b/frontend/src/utils/icons.tsx
@@ -63,12 +63,3 @@ export const CircleIcon = Circle;
 
 // Export type for icon props
 export type { LucideProps as IconProps };
-
-// Default icon size classes
-export const iconSizes = {
-  xs: "w-3 h-3",
-  sm: "w-4 h-4",
-  md: "w-5 h-5",
-  lg: "w-6 h-6",
-  xl: "w-8 h-8",
-} as const;

From 14c8f2a845197e6ee09ad4891af7dc0e02b39be8 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:08:06 -0700
Subject: [PATCH 115/173] Frontend: Add basic react/dom tests

---
 frontend/tests/components/S3Browser.test.tsx | 117 ++++++++++
 frontend/tests/components/Stepper.test.tsx   | 135 +++++++++++
 frontend/tests/components/common.test.tsx    | 225 +++++++++++++++++++
 frontend/tests/components/layout.test.tsx    | 112 +++++++++
 frontend/tests/components/settings.test.tsx  |  82 +++++++
 frontend/tests/hooks/useDebounce.test.ts     |  91 ++++++++
 frontend/tests/hooks/usePagination.test.ts   | 121 ++++++++++
 frontend/tests/hooks/useSSE.test.ts          | 177 +++++++++++++++
 frontend/tests/setup.ts                      |   1 +
 frontend/tests/utils/formatters.test.ts      | 110 +++++++++
 frontend/vitest.config.ts                    |  12 +
 11 files changed, 1183 insertions(+)
 create mode 100644 frontend/tests/components/S3Browser.test.tsx
 create mode 100644 frontend/tests/components/Stepper.test.tsx
 create mode 100644 frontend/tests/components/common.test.tsx
 create mode 100644 frontend/tests/components/layout.test.tsx
 create mode 100644 frontend/tests/components/settings.test.tsx
 create mode 100644 frontend/tests/hooks/useDebounce.test.ts
 create mode 100644 frontend/tests/hooks/usePagination.test.ts
 create mode 100644 frontend/tests/hooks/useSSE.test.ts
 create mode 100644 frontend/tests/setup.ts
 create mode 100644 frontend/tests/utils/formatters.test.ts
 create mode 100644 frontend/vitest.config.ts

diff --git a/frontend/tests/components/S3Browser.test.tsx b/frontend/tests/components/S3Browser.test.tsx
new file mode 100644
index 0000000..497ce3b
--- /dev/null
+++ b/frontend/tests/components/S3Browser.test.tsx
@@ -0,0 +1,117 @@
+import { render, screen, waitFor } from "@testing-library/react";
+import userEvent from "@testing-library/user-event";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import S3Browser from "../../src/components/files/S3Browser.tsx";
+
+// Mock the API client
+vi.mock("../../src/api/client.ts", () => ({
+  apiGet: vi.fn(),
+}));
+
+import { apiGet } from "../../src/api/client.ts";
+
+const mockApiGet = vi.mocked(apiGet);
+
+const MOCK_LIST_RESPONSE = {
+  success: true,
+  folders: [
+    { name: "year=2024", prefix: "year=2024/" },
+    { name: "year=2025", prefix: "year=2025/" },
+  ],
+  files: [
+    { name: "test.mcap", key: "test.mcap", size: 1024, last_modified: "2024-01-15T10:30:00Z" },
+  ],
+  breadcrumbs: [],
+};
+
+const MOCK_SUBFOLDER_RESPONSE = {
+  success: true,
+  folders: [
+    { name: "month=01", prefix: "year=2024/month=01/" },
+    { name: "month=02", prefix: "year=2024/month=02/" },
+  ],
+  files: [],
+  breadcrumbs: [{ name: "year=2024", prefix: "year=2024/" }],
+};
+
+describe("S3Browser", () => {
+  beforeEach(() => {
+    mockApiGet.mockReset();
+  });
+
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  it("shows loading spinner initially", () => {
+    mockApiGet.mockReturnValue(new Promise(() => {})); // Never resolves
+    render(<S3Browser bucketName="my-bucket" region="us-west-2" />);
+    expect(screen.getByText("Loading files...")).toBeInTheDocument();
+  });
+
+  it("renders bucket name and region", async () => {
+    mockApiGet.mockResolvedValue(MOCK_LIST_RESPONSE);
+    render(<S3Browser bucketName="my-bucket" region="us-west-2" />);
+
+    await waitFor(() => {
+      expect(screen.getAllByText("my-bucket").length).toBeGreaterThanOrEqual(1);
+    });
+    expect(screen.getByText("(us-west-2)")).toBeInTheDocument();
+  });
+
+  it("renders folders and files from the API response", async () => {
+    mockApiGet.mockResolvedValue(MOCK_LIST_RESPONSE);
+    render(<S3Browser bucketName="my-bucket" region="us-west-2" />);
+
+    await waitFor(() => {
+      expect(screen.getByText("year=2024")).toBeInTheDocument();
+    });
+    expect(screen.getByText("year=2025")).toBeInTheDocument();
+    expect(screen.getByText("test.mcap")).toBeInTheDocument();
+    expect(screen.getByText("1.0 KB")).toBeInTheDocument();
+  });
+
+  it("navigates into a folder when clicked", async () => {
+    const user = userEvent.setup();
+    mockApiGet
+      .mockResolvedValueOnce(MOCK_LIST_RESPONSE) // Initial load
+      .mockResolvedValueOnce(MOCK_SUBFOLDER_RESPONSE); // After click
+
+    render(<S3Browser bucketName="my-bucket" region="us-west-2" />);
+
+    await waitFor(() => {
+      expect(screen.getByText("year=2024")).toBeInTheDocument();
+    });
+
+    await user.click(screen.getByText("year=2024"));
+
+    await waitFor(() => {
+      expect(screen.getByText("month=01")).toBeInTheDocument();
+    });
+    expect(screen.getByText("month=02")).toBeInTheDocument();
+  });
+
+  it("shows an error message and retry button on API failure", async () => {
+    mockApiGet.mockRejectedValue(new Error("Network error"));
+    render(<S3Browser bucketName="my-bucket" region="us-west-2" />);
+
+    await waitFor(() => {
+      expect(screen.getByText("Network error")).toBeInTheDocument();
+    });
+    expect(screen.getByText("Retry")).toBeInTheDocument();
+  });
+
+  it("shows empty state when no files or folders", async () => {
+    mockApiGet.mockResolvedValue({
+      success: true,
+      folders: [],
+      files: [],
+      breadcrumbs: [],
+    });
+    render(<S3Browser bucketName="my-bucket" region="us-west-2" />);
+
+    await waitFor(() => {
+      expect(screen.getByText("No files or folders found at this location.")).toBeInTheDocument();
+    });
+  });
+});
diff --git a/frontend/tests/components/Stepper.test.tsx b/frontend/tests/components/Stepper.test.tsx
new file mode 100644
index 0000000..c554c35
--- /dev/null
+++ b/frontend/tests/components/Stepper.test.tsx
@@ -0,0 +1,135 @@
+/**
+ * Tests for the Stepper component.
+ */
+
+import { render, screen, cleanup } from "@testing-library/react";
+import userEvent from "@testing-library/user-event";
+import { describe, it, expect, vi, afterEach } from "vitest";
+
+import Stepper from "../../src/components/upload/Stepper.tsx";
+
+afterEach(() => {
+  cleanup();
+});
+
+describe("Stepper", () => {
+  it("renders all four steps", () => {
+    render(<Stepper currentStep={1} />);
+
+    expect(screen.getByTestId("step-1")).toBeInTheDocument();
+    expect(screen.getByTestId("step-2")).toBeInTheDocument();
+    expect(screen.getByTestId("step-3")).toBeInTheDocument();
+    expect(screen.getByTestId("step-4")).toBeInTheDocument();
+  });
+
+  it("displays step labels", () => {
+    render(<Stepper currentStep={1} />);
+
+    expect(screen.getByText("Select")).toBeInTheDocument();
+    expect(screen.getByText("Review")).toBeInTheDocument();
+    expect(screen.getByText("Upload")).toBeInTheDocument();
+    expect(screen.getByText("Complete")).toBeInTheDocument();
+  });
+
+  it("marks the current step as active", () => {
+    render(<Stepper currentStep={2} />);
+
+    const step2 = screen.getByTestId("step-2");
+    expect(step2).toHaveAttribute("aria-current", "step");
+  });
+
+  it("shows checkmark icon for completed steps", () => {
+    render(<Stepper currentStep={3} />);
+
+    // Steps 1 and 2 should have checkmarks
+    const checkmarks = screen.getAllByTestId("checkmark-icon");
+    expect(checkmarks).toHaveLength(2);
+  });
+
+  it("shows numbers for active and future steps", () => {
+    render(<Stepper currentStep={2} />);
+
+    // Step 2 (active) should show "2"
+    expect(screen.getByTestId("step-2")).toHaveTextContent("2");
+    // Step 3 (future) should show "3"
+    expect(screen.getByTestId("step-3")).toHaveTextContent("3");
+    // Step 4 (future) should show "4"
+    expect(screen.getByTestId("step-4")).toHaveTextContent("4");
+  });
+
+  it("allows clicking completed steps 1 and 2 when not uploading", async () => {
+    const user = userEvent.setup();
+    const onStepClick = vi.fn();
+
+    render(
+      <Stepper currentStep={3} onStepClick={onStepClick} isUploading={false} />,
+    );
+
+    // Step 1 (completed) should be clickable
+    await user.click(screen.getByTestId("step-1"));
+    expect(onStepClick).toHaveBeenCalledWith(1);
+
+    // Step 2 (completed) should be clickable
+    await user.click(screen.getByTestId("step-2"));
+    expect(onStepClick).toHaveBeenCalledWith(2);
+  });
+
+  it("disables clicking completed steps when uploading", async () => {
+    const user = userEvent.setup();
+    const onStepClick = vi.fn();
+
+    render(
+      <Stepper currentStep={3} onStepClick={onStepClick} isUploading={true} />,
+    );
+
+    // Step 1 should be disabled
+    const step1 = screen.getByTestId("step-1");
+    expect(step1).toBeDisabled();
+
+    await user.click(step1);
+    expect(onStepClick).not.toHaveBeenCalled();
+  });
+
+  it("does not allow clicking future steps", async () => {
+    const user = userEvent.setup();
+    const onStepClick = vi.fn();
+
+    render(
+      <Stepper currentStep={1} onStepClick={onStepClick} />,
+    );
+
+    // Step 3 (future) should be disabled
+    const step3 = screen.getByTestId("step-3");
+    expect(step3).toBeDisabled();
+
+    await user.click(step3);
+    expect(onStepClick).not.toHaveBeenCalled();
+  });
+
+  it("does not allow clicking the active step", async () => {
+    const user = userEvent.setup();
+    const onStepClick = vi.fn();
+
+    render(
+      <Stepper currentStep={2} onStepClick={onStepClick} />,
+    );
+
+    const step2 = screen.getByTestId("step-2");
+    expect(step2).toBeDisabled();
+
+    await user.click(step2);
+    expect(onStepClick).not.toHaveBeenCalled();
+  });
+
+  it("step 4 renders at correct position", () => {
+    render(<Stepper currentStep={4} />);
+
+    // All four previous steps should have checkmarks
+    const checkmarks = screen.getAllByTestId("checkmark-icon");
+    expect(checkmarks).toHaveLength(3); // Steps 1, 2, 3
+
+    // Step 4 is active
+    const step4 = screen.getByTestId("step-4");
+    expect(step4).toHaveAttribute("aria-current", "step");
+  });
+});
diff --git a/frontend/tests/components/common.test.tsx b/frontend/tests/components/common.test.tsx
new file mode 100644
index 0000000..eac956a
--- /dev/null
+++ b/frontend/tests/components/common.test.tsx
@@ -0,0 +1,225 @@
+import { render, screen } from "@testing-library/react";
+import userEvent from "@testing-library/user-event";
+import { describe, expect, it, vi } from "vitest";
+import Modal from "../../src/components/common/Modal.tsx";
+import ProgressBar from "../../src/components/common/ProgressBar.tsx";
+import StatCard from "../../src/components/common/StatCard.tsx";
+import Breadcrumb from "../../src/components/common/Breadcrumb.tsx";
+import Spinner from "../../src/components/common/Spinner.tsx";
+import SortableHeader from "../../src/components/common/SortableHeader.tsx";
+
+describe("Modal", () => {
+  it("renders nothing when isOpen is false", () => {
+    render(
+      <Modal isOpen={false} onClose={() => {}} title="Test">
+        <p>body</p>
+      </Modal>,
+    );
+    expect(screen.queryByText("Test")).not.toBeInTheDocument();
+  });
+
+  it("renders title, body, and footer when open", () => {
+    render(
+      <Modal isOpen={true} onClose={() => {}} title="My Modal" footer={<button>OK</button>}>
+        <p>Hello world</p>
+      </Modal>,
+    );
+    expect(screen.getByText("My Modal")).toBeInTheDocument();
+    expect(screen.getByText("Hello world")).toBeInTheDocument();
+    expect(screen.getByText("OK")).toBeInTheDocument();
+  });
+
+  it("calls onClose when Escape is pressed", async () => {
+    const user = userEvent.setup();
+    const handleClose = vi.fn();
+    render(
+      <Modal isOpen={true} onClose={handleClose} title="Test">
+        <p>content</p>
+      </Modal>,
+    );
+
+    await user.keyboard("{Escape}");
+    expect(handleClose).toHaveBeenCalledOnce();
+  });
+
+  it("calls onClose when backdrop is clicked", async () => {
+    const user = userEvent.setup();
+    const handleClose = vi.fn();
+    render(
+      <Modal isOpen={true} onClose={handleClose} title="Test">
+        <p>content</p>
+      </Modal>,
+    );
+
+    await user.click(screen.getByTestId("modal-backdrop"));
+    expect(handleClose).toHaveBeenCalledOnce();
+  });
+
+  it("does not call onClose when modal content is clicked", async () => {
+    const user = userEvent.setup();
+    const handleClose = vi.fn();
+    render(
+      <Modal isOpen={true} onClose={handleClose} title="Test">
+        <p>content</p>
+      </Modal>,
+    );
+
+    await user.click(screen.getByText("content"));
+    expect(handleClose).not.toHaveBeenCalled();
+  });
+
+  it("calls onClose when close button (X) is clicked", async () => {
+    const user = userEvent.setup();
+    const handleClose = vi.fn();
+    render(
+      <Modal isOpen={true} onClose={handleClose} title="Test">
+        <p>content</p>
+      </Modal>,
+    );
+
+    await user.click(screen.getByLabelText("Close modal"));
+    expect(handleClose).toHaveBeenCalledOnce();
+  });
+});
+
+describe("StatCard", () => {
+  it("renders value and label", () => {
+    render(<StatCard value={42} label="Total Files" />);
+    expect(screen.getByText("42")).toBeInTheDocument();
+    expect(screen.getByText("Total Files")).toBeInTheDocument();
+  });
+
+  it("renders string values", () => {
+    render(<StatCard value="1.5 GB" label="Total Size" />);
+    expect(screen.getByText("1.5 GB")).toBeInTheDocument();
+    expect(screen.getByText("Total Size")).toBeInTheDocument();
+  });
+
+  it("applies default text color to value", () => {
+    render(<StatCard value={0} label="Test" />);
+    const value = screen.getByText("0");
+    expect(value.className).toContain("text-nlr-blue");
+  });
+
+  it("applies custom text color to value", () => {
+    render(<StatCard value={0} label="Test" color="text-red-500" />);
+    const value = screen.getByText("0");
+    expect(value.className).toContain("text-red-500");
+  });
+});
+
+describe("ProgressBar", () => {
+  it("shows correct width style", () => {
+    render(<ProgressBar percent={65} />);
+    const bar = screen.getByRole("progressbar");
+    expect(bar).toHaveStyle({ width: "65%" });
+  });
+
+  it("shows percentage text when label is provided", () => {
+    render(<ProgressBar percent={42} label="Uploading" />);
+    expect(screen.getByText("Uploading")).toBeInTheDocument();
+    expect(screen.getByText("42%")).toBeInTheDocument();
+  });
+
+  it("clamps percent to 0-100 range", () => {
+    render(<ProgressBar percent={150} />);
+    const bar = screen.getByRole("progressbar");
+    expect(bar).toHaveStyle({ width: "100%" });
+    expect(bar.getAttribute("aria-valuenow")).toBe("100");
+  });
+
+  it("clamps negative percent to 0", () => {
+    render(<ProgressBar percent={-10} />);
+    const bar = screen.getByRole("progressbar");
+    expect(bar).toHaveStyle({ width: "0%" });
+    expect(bar.getAttribute("aria-valuenow")).toBe("0");
+  });
+
+  it("applies default color", () => {
+    render(<ProgressBar percent={50} />);
+    const bar = screen.getByRole("progressbar");
+    expect(bar.className).toContain("bg-nlr-blue");
+  });
+});
+
+describe("Breadcrumb", () => {
+  it("renders all items", () => {
+    render(
+      <Breadcrumb
+        items={[
+          { label: "Home", onClick: () => {} },
+          { label: "Files", onClick: () => {} },
+          { label: "Current" },
+        ]}
+      />,
+    );
+    expect(screen.getByText("Home")).toBeInTheDocument();
+    expect(screen.getByText("Files")).toBeInTheDocument();
+    expect(screen.getByText("Current")).toBeInTheDocument();
+  });
+
+  it("makes the last item non-clickable", () => {
+    render(
+      <Breadcrumb
+        items={[
+          { label: "Home", onClick: () => {} },
+          { label: "Current" },
+        ]}
+      />,
+    );
+    // Last item should be a span, not a button
+    expect(screen.getByText("Current").tagName).toBe("SPAN");
+    // First item should be a button
+    expect(screen.getByText("Home").tagName).toBe("BUTTON");
+  });
+
+  it("calls onClick when a breadcrumb item is clicked", async () => {
+    const user = userEvent.setup();
+    const handleClick = vi.fn();
+    render(
+      <Breadcrumb
+        items={[
+          { label: "Home", onClick: handleClick },
+          { label: "Current" },
+        ]}
+      />,
+    );
+
+    await user.click(screen.getByText("Home"));
+    expect(handleClick).toHaveBeenCalledOnce();
+  });
+});
+
+describe("Spinner", () => {
+  it("renders without a message", () => {
+    render(<Spinner />);
+    expect(screen.getByTestId("spinner")).toBeInTheDocument();
+  });
+
+  it("renders with a message", () => {
+    render(<Spinner message="Loading data..." />);
+    expect(screen.getByText("Loading data...")).toBeInTheDocument();
+  });
+});
+
+describe("SortableHeader", () => {
+  it("renders label and calls onSort when clicked", async () => {
+    const user = userEvent.setup();
+    const handleSort = vi.fn();
+    const { container } = render(
+      <table>
+        <thead>
+          <tr>
+            <SortableHeader label="Name" active={false} ascending={true} onSort={handleSort} />
+          </tr>
+        </thead>
+      </table>,
+    );
+    expect(screen.getByText("Name")).toBeInTheDocument();
+
+    const th = container.querySelector("th");
+    expect(th).not.toBeNull();
+    await user.click(th!);
+    expect(handleSort).toHaveBeenCalledOnce();
+  });
+});
diff --git a/frontend/tests/components/layout.test.tsx b/frontend/tests/components/layout.test.tsx
new file mode 100644
index 0000000..cdafec8
--- /dev/null
+++ b/frontend/tests/components/layout.test.tsx
@@ -0,0 +1,112 @@
+import { render, screen } from "@testing-library/react";
+import userEvent from "@testing-library/user-event";
+import { MemoryRouter } from "react-router-dom";
+import { describe, expect, it, vi, beforeEach } from "vitest";
+import Layout from "../../src/components/layout/Layout.tsx";
+import NavBar from "../../src/components/layout/NavBar.tsx";
+import { useAppStore } from "../../src/stores/appStore.ts";
+
+// Mock react-router-dom's Outlet so Layout renders without child routes
+vi.mock("react-router-dom", async () => {
+  const actual = await vi.importActual<typeof import("react-router-dom")>("react-router-dom");
+  return {
+    ...actual,
+    Outlet: () => <div data-testid="outlet">page content</div>,
+  };
+});
+
+function renderWithRouter(ui: React.ReactElement) {
+  return render(<MemoryRouter>{ui}</MemoryRouter>);
+}
+
+describe("Layout", () => {
+  beforeEach(() => {
+    useAppStore.setState({
+      settings: null,
+      version: { version: "1.2.3", commit: "abc1234def5678", branch: "main", dirty: false },
+      notifications: [],
+    });
+  });
+
+  it("renders Header, NavBar, Footer, and Outlet", () => {
+    renderWithRouter(<Layout />);
+
+    // Header - title defaults to MODAQ Upload when settings are null
+    expect(screen.getByText("MODAQ Upload")).toBeInTheDocument();
+
+    // NavBar links
+    expect(screen.getByText("Upload")).toBeInTheDocument();
+    expect(screen.getByText("Browse Uploaded Files")).toBeInTheDocument();
+    expect(screen.getByText("History")).toBeInTheDocument();
+    expect(screen.getByText("Settings")).toBeInTheDocument();
+
+    // Footer
+    expect(screen.getByText("National Laboratory of the Rockies")).toBeInTheDocument();
+
+    // Outlet (mocked)
+    expect(screen.getByTestId("outlet")).toBeInTheDocument();
+  });
+
+  it("opens AboutModal when version badge is clicked", async () => {
+    const user = userEvent.setup();
+    renderWithRouter(<Layout />);
+
+    const badge = screen.getByText("v1.2.3");
+    await user.click(badge);
+
+    // Modal should now be open - check for the modal backdrop and version info
+    expect(screen.getByTestId("modal-backdrop")).toBeInTheDocument();
+    expect(screen.getByRole("heading", { name: "About" })).toBeInTheDocument();
+    expect(screen.getByText("1.2.3")).toBeInTheDocument();
+    expect(screen.getByText("abc1234")).toBeInTheDocument();
+  });
+
+  it("closes AboutModal when close button is clicked", async () => {
+    const user = userEvent.setup();
+    renderWithRouter(<Layout />);
+
+    await user.click(screen.getByText("v1.2.3"));
+    expect(screen.getByTestId("modal-backdrop")).toBeInTheDocument();
+
+    // Click the footer Close button
+    const closeButtons = screen.getAllByText("Close");
+    await user.click(closeButtons[0]);
+    expect(screen.queryByTestId("modal-backdrop")).not.toBeInTheDocument();
+  });
+});
+
+describe("NavBar", () => {
+  beforeEach(() => {
+    useAppStore.setState({
+      version: { version: "2.0.0", commit: "deadbeef", branch: "develop", dirty: false },
+    });
+  });
+
+  it("shows all 4 nav links", () => {
+    renderWithRouter(<NavBar onAboutClick={() => {}} />);
+
+    expect(screen.getByText("Upload")).toBeInTheDocument();
+    expect(screen.getByText("Browse Uploaded Files")).toBeInTheDocument();
+    expect(screen.getByText("History")).toBeInTheDocument();
+    expect(screen.getByText("Settings")).toBeInTheDocument();
+  });
+
+  it("shows version badge and calls onAboutClick when clicked", async () => {
+    const user = userEvent.setup();
+    const handleAboutClick = vi.fn();
+    renderWithRouter(<NavBar onAboutClick={handleAboutClick} />);
+
+    const badge = screen.getByText("v2.0.0");
+    expect(badge).toBeInTheDocument();
+
+    await user.click(badge);
+    expect(handleAboutClick).toHaveBeenCalledOnce();
+  });
+
+  it("hides version badge when version is not loaded", () => {
+    useAppStore.setState({ version: null });
+    renderWithRouter(<NavBar onAboutClick={() => {}} />);
+
+    expect(screen.queryByText(/^v/)).not.toBeInTheDocument();
+  });
+});
diff --git a/frontend/tests/components/settings.test.tsx b/frontend/tests/components/settings.test.tsx
new file mode 100644
index 0000000..62330c5
--- /dev/null
+++ b/frontend/tests/components/settings.test.tsx
@@ -0,0 +1,82 @@
+import { describe, it, expect, vi, beforeEach } from "vitest";
+import { render, screen, waitFor } from "@testing-library/react";
+import SettingsForm from "../../src/components/settings/SettingsForm.tsx";
+import { useAppStore } from "../../src/stores/appStore.ts";
+
+// Mock the API client
+vi.mock("../../src/api/client.ts", () => ({
+  apiGet: vi.fn(),
+  apiPost: vi.fn(),
+  apiPut: vi.fn(),
+}));
+
+// Import mocked functions for control
+import { apiGet } from "../../src/api/client.ts";
+
+const mockApiGet = vi.mocked(apiGet);
+
+describe("SettingsForm", () => {
+  beforeEach(() => {
+    vi.clearAllMocks();
+
+    // Set up store with settings
+    useAppStore.setState({
+      settings: {
+        aws_profile: "default",
+        aws_region: "us-west-2",
+        s3_bucket: "test-bucket",
+        default_upload_folder: "/data/mcap",
+        display_name: "Test App",
+        log_directory: "logs",
+      },
+      settingsLoading: false,
+    });
+
+    // Mock profiles endpoint
+    mockApiGet.mockResolvedValue({ profiles: ["default", "production"] });
+  });
+
+  it("renders all form fields", async () => {
+    render(<SettingsForm />);
+
+    await waitFor(() => {
+      expect(screen.getByLabelText("AWS Profile")).toBeInTheDocument();
+    });
+
+    expect(screen.getByLabelText("AWS Region")).toBeInTheDocument();
+    expect(screen.getByLabelText("S3 Bucket")).toBeInTheDocument();
+    expect(screen.getByLabelText("Default Upload Folder")).toBeInTheDocument();
+    expect(screen.getByLabelText("Display Name")).toBeInTheDocument();
+    expect(screen.getByLabelText("Log Directory")).toBeInTheDocument();
+  });
+
+  it("shows Test Connection and Save Settings buttons", async () => {
+    render(<SettingsForm />);
+
+    await waitFor(() => {
+      expect(screen.getByText("Test Connection")).toBeInTheDocument();
+    });
+
+    expect(screen.getByText("Save Settings")).toBeInTheDocument();
+  });
+
+  it("populates form fields from settings", async () => {
+    render(<SettingsForm />);
+
+    await waitFor(() => {
+      expect(screen.getByLabelText("S3 Bucket")).toHaveValue("test-bucket");
+    });
+
+    expect(screen.getByLabelText("Default Upload Folder")).toHaveValue("/data/mcap");
+    expect(screen.getByLabelText("Display Name")).toHaveValue("Test App");
+    expect(screen.getByLabelText("Log Directory")).toHaveValue("logs");
+  });
+
+  it("fetches profiles on mount", async () => {
+    render(<SettingsForm />);
+
+    await waitFor(() => {
+      expect(mockApiGet).toHaveBeenCalledWith("/api/settings/profiles");
+    });
+  });
+});
diff --git a/frontend/tests/hooks/useDebounce.test.ts b/frontend/tests/hooks/useDebounce.test.ts
new file mode 100644
index 0000000..ac9ee75
--- /dev/null
+++ b/frontend/tests/hooks/useDebounce.test.ts
@@ -0,0 +1,91 @@
+import { act, renderHook } from "@testing-library/react";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import { useDebounce } from "../../src/hooks/useDebounce.ts";
+
+describe("useDebounce", () => {
+  beforeEach(() => {
+    vi.useFakeTimers();
+  });
+
+  afterEach(() => {
+    vi.useRealTimers();
+  });
+
+  it("returns the initial value immediately", () => {
+    const { result } = renderHook(() => useDebounce("hello", 300));
+    expect(result.current).toBe("hello");
+  });
+
+  it("does not update the debounced value before the delay", () => {
+    const { result, rerender } = renderHook(({ value }) => useDebounce(value, 300), {
+      initialProps: { value: "hello" },
+    });
+
+    rerender({ value: "world" });
+
+    act(() => {
+      vi.advanceTimersByTime(100);
+    });
+
+    expect(result.current).toBe("hello");
+  });
+
+  it("updates the debounced value after the delay", () => {
+    const { result, rerender } = renderHook(({ value }) => useDebounce(value, 300), {
+      initialProps: { value: "hello" },
+    });
+
+    rerender({ value: "world" });
+
+    act(() => {
+      vi.advanceTimersByTime(300);
+    });
+
+    expect(result.current).toBe("world");
+  });
+
+  it("uses the default delay of 300ms", () => {
+    const { result, rerender } = renderHook(({ value }) => useDebounce(value), {
+      initialProps: { value: "a" },
+    });
+
+    rerender({ value: "b" });
+
+    act(() => {
+      vi.advanceTimersByTime(299);
+    });
+    expect(result.current).toBe("a");
+
+    act(() => {
+      vi.advanceTimersByTime(1);
+    });
+    expect(result.current).toBe("b");
+  });
+
+  it("resets the timer on rapid changes and only takes the last value", () => {
+    const { result, rerender } = renderHook(({ value }) => useDebounce(value, 200), {
+      initialProps: { value: "a" },
+    });
+
+    rerender({ value: "b" });
+    act(() => {
+      vi.advanceTimersByTime(100);
+    });
+
+    rerender({ value: "c" });
+    act(() => {
+      vi.advanceTimersByTime(100);
+    });
+
+    // Still the initial value since each change reset the timer
+    expect(result.current).toBe("a");
+
+    rerender({ value: "d" });
+    act(() => {
+      vi.advanceTimersByTime(200);
+    });
+
+    // Now it should be the latest value
+    expect(result.current).toBe("d");
+  });
+});
diff --git a/frontend/tests/hooks/usePagination.test.ts b/frontend/tests/hooks/usePagination.test.ts
new file mode 100644
index 0000000..c14eb94
--- /dev/null
+++ b/frontend/tests/hooks/usePagination.test.ts
@@ -0,0 +1,121 @@
+import { act, renderHook } from "@testing-library/react";
+import { describe, expect, it } from "vitest";
+import { usePagination } from "../../src/hooks/usePagination.ts";
+
+describe("usePagination", () => {
+  it("starts at page 1 with default limit of 100", () => {
+    const { result } = renderHook(() => usePagination());
+    expect(result.current.currentPage).toBe(1);
+    expect(result.current.limit).toBe(100);
+    expect(result.current.offset).toBe(0);
+    expect(result.current.totalPages).toBe(1);
+  });
+
+  it("respects custom page size", () => {
+    const { result } = renderHook(() => usePagination(25));
+    expect(result.current.limit).toBe(25);
+  });
+
+  it("computes totalPages when setTotal is called", () => {
+    const { result } = renderHook(() => usePagination(50));
+    act(() => {
+      result.current.setTotal(120);
+    });
+    expect(result.current.totalPages).toBe(3); // ceil(120/50)
+  });
+
+  it("navigates with nextPage and prevPage", () => {
+    const { result } = renderHook(() => usePagination(10));
+    act(() => {
+      result.current.setTotal(50);
+    });
+    expect(result.current.totalPages).toBe(5);
+
+    act(() => {
+      result.current.nextPage();
+    });
+    expect(result.current.currentPage).toBe(2);
+    expect(result.current.offset).toBe(10);
+
+    act(() => {
+      result.current.nextPage();
+    });
+    expect(result.current.currentPage).toBe(3);
+    expect(result.current.offset).toBe(20);
+
+    act(() => {
+      result.current.prevPage();
+    });
+    expect(result.current.currentPage).toBe(2);
+    expect(result.current.offset).toBe(10);
+  });
+
+  it("does not go below page 1", () => {
+    const { result } = renderHook(() => usePagination(10));
+    act(() => {
+      result.current.setTotal(30);
+    });
+    act(() => {
+      result.current.prevPage();
+    });
+    expect(result.current.currentPage).toBe(1);
+  });
+
+  it("does not go above totalPages", () => {
+    const { result } = renderHook(() => usePagination(10));
+    act(() => {
+      result.current.setTotal(20);
+    });
+    // totalPages = 2
+    act(() => {
+      result.current.goToPage(5);
+    });
+    expect(result.current.currentPage).toBe(2);
+  });
+
+  it("goToPage navigates to the correct page", () => {
+    const { result } = renderHook(() => usePagination(10));
+    act(() => {
+      result.current.setTotal(100);
+    });
+    act(() => {
+      result.current.goToPage(7);
+    });
+    expect(result.current.currentPage).toBe(7);
+    expect(result.current.offset).toBe(60);
+  });
+
+  it("clamps current page when total shrinks", () => {
+    const { result } = renderHook(() => usePagination(10));
+    act(() => {
+      result.current.setTotal(100);
+    });
+    act(() => {
+      result.current.goToPage(10);
+    });
+    expect(result.current.currentPage).toBe(10);
+
+    act(() => {
+      result.current.setTotal(30);
+    });
+    // totalPages = 3, so page should clamp to 3
+    expect(result.current.currentPage).toBe(3);
+  });
+
+  it("reset goes back to page 1", () => {
+    const { result } = renderHook(() => usePagination(10));
+    act(() => {
+      result.current.setTotal(50);
+    });
+    act(() => {
+      result.current.goToPage(4);
+    });
+    expect(result.current.currentPage).toBe(4);
+
+    act(() => {
+      result.current.reset();
+    });
+    expect(result.current.currentPage).toBe(1);
+    expect(result.current.offset).toBe(0);
+  });
+});
diff --git a/frontend/tests/hooks/useSSE.test.ts b/frontend/tests/hooks/useSSE.test.ts
new file mode 100644
index 0000000..ffe78b6
--- /dev/null
+++ b/frontend/tests/hooks/useSSE.test.ts
@@ -0,0 +1,177 @@
+/**
+ * Tests for the useSSE hook.
+ */
+
+import { renderHook, act, cleanup } from "@testing-library/react";
+import { describe, it, expect, vi, beforeEach, afterEach } from "vitest";
+
+import { useSSE } from "../../src/hooks/useSSE.ts";
+
+// Mock EventSource
+class MockEventSource {
+  url: string;
+  onmessage: ((event: MessageEvent) => void) | null = null;
+  onerror: ((event: Event) => void) | null = null;
+  readyState = 0;
+  closed = false;
+
+  constructor(url: string) {
+    this.url = url;
+    MockEventSource.instances.push(this);
+  }
+
+  close() {
+    this.closed = true;
+    this.readyState = 2;
+  }
+
+  // Simulate a message from the server
+  simulateMessage(data: unknown) {
+    if (this.onmessage) {
+      this.onmessage(new MessageEvent("message", { data: JSON.stringify(data) }));
+    }
+  }
+
+  // Simulate an error
+  simulateError() {
+    if (this.onerror) {
+      this.onerror(new Event("error"));
+    }
+  }
+
+  static instances: MockEventSource[] = [];
+  static clear() {
+    MockEventSource.instances = [];
+  }
+}
+
+// Install mock
+beforeEach(() => {
+  MockEventSource.clear();
+  vi.stubGlobal("EventSource", MockEventSource);
+});
+
+afterEach(() => {
+  cleanup();
+  vi.restoreAllMocks();
+});
+
+describe("useSSE", () => {
+  it("does not create an EventSource when url is null", () => {
+    const onMessage = vi.fn();
+    renderHook(() => useSSE({ url: null, onMessage }));
+
+    expect(MockEventSource.instances).toHaveLength(0);
+  });
+
+  it("creates an EventSource when url is provided", () => {
+    const onMessage = vi.fn();
+    renderHook(() =>
+      useSSE({ url: "/api/upload/progress/test-id", onMessage }),
+    );
+
+    expect(MockEventSource.instances).toHaveLength(1);
+    expect(MockEventSource.instances[0]!.url).toBe(
+      "/api/upload/progress/test-id",
+    );
+  });
+
+  it("calls onMessage with parsed JSON data", () => {
+    const onMessage = vi.fn();
+    renderHook(() =>
+      useSSE({ url: "/api/upload/progress/test-id", onMessage }),
+    );
+
+    const es = MockEventSource.instances[0]!;
+    act(() => {
+      es.simulateMessage({ type: "scan_started", folders_total: 5 });
+    });
+
+    expect(onMessage).toHaveBeenCalledTimes(1);
+    expect(onMessage).toHaveBeenCalledWith({
+      type: "scan_started",
+      folders_total: 5,
+    });
+  });
+
+  it("ignores non-JSON messages without throwing", () => {
+    const onMessage = vi.fn();
+    renderHook(() =>
+      useSSE({ url: "/api/upload/progress/test-id", onMessage }),
+    );
+
+    const es = MockEventSource.instances[0]!;
+    // Send raw non-JSON string
+    act(() => {
+      if (es.onmessage) {
+        es.onmessage(new MessageEvent("message", { data: "not-json" }));
+      }
+    });
+
+    expect(onMessage).not.toHaveBeenCalled();
+  });
+
+  it("calls onError and closes on error", () => {
+    const onMessage = vi.fn();
+    const onError = vi.fn();
+    renderHook(() =>
+      useSSE({ url: "/api/upload/progress/test-id", onMessage, onError }),
+    );
+
+    const es = MockEventSource.instances[0]!;
+    act(() => {
+      es.simulateError();
+    });
+
+    expect(onError).toHaveBeenCalledTimes(1);
+    expect(es.closed).toBe(true);
+  });
+
+  it("closes the EventSource on unmount", () => {
+    const onMessage = vi.fn();
+    const { unmount } = renderHook(() =>
+      useSSE({ url: "/api/upload/progress/test-id", onMessage }),
+    );
+
+    const es = MockEventSource.instances[0]!;
+    expect(es.closed).toBe(false);
+
+    unmount();
+
+    expect(es.closed).toBe(true);
+  });
+
+  it("closes old EventSource and opens new one when url changes", () => {
+    const onMessage = vi.fn();
+    const { rerender } = renderHook(
+      ({ url }: { url: string | null }) => useSSE({ url, onMessage }),
+      { initialProps: { url: "/api/upload/progress/id-1" } },
+    );
+
+    expect(MockEventSource.instances).toHaveLength(1);
+    const first = MockEventSource.instances[0]!;
+
+    rerender({ url: "/api/upload/progress/id-2" });
+
+    expect(first.closed).toBe(true);
+    expect(MockEventSource.instances).toHaveLength(2);
+    expect(MockEventSource.instances[1]!.url).toBe(
+      "/api/upload/progress/id-2",
+    );
+  });
+
+  it("closes EventSource when url changes to null", () => {
+    const onMessage = vi.fn();
+    const { rerender } = renderHook(
+      ({ url }: { url: string | null }) => useSSE({ url, onMessage }),
+      { initialProps: { url: "/api/upload/progress/id-1" as string | null } },
+    );
+
+    const es = MockEventSource.instances[0]!;
+    expect(es.closed).toBe(false);
+
+    rerender({ url: null });
+
+    expect(es.closed).toBe(true);
+  });
+});
diff --git a/frontend/tests/setup.ts b/frontend/tests/setup.ts
new file mode 100644
index 0000000..f149f27
--- /dev/null
+++ b/frontend/tests/setup.ts
@@ -0,0 +1 @@
+import "@testing-library/jest-dom/vitest";
diff --git a/frontend/tests/utils/formatters.test.ts b/frontend/tests/utils/formatters.test.ts
new file mode 100644
index 0000000..5d4b4c8
--- /dev/null
+++ b/frontend/tests/utils/formatters.test.ts
@@ -0,0 +1,110 @@
+import { describe, it, expect } from "vitest";
+import { formatBytes } from "../../src/utils/format/bytes.ts";
+import { formatDate, formatDateTime } from "../../src/utils/format/date.ts";
+import { formatDuration, formatEta } from "../../src/utils/format/time.ts";
+
+describe("formatBytes", () => {
+  it('returns "0 B" for zero bytes', () => {
+    expect(formatBytes(0)).toBe("0 B");
+  });
+
+  it("formats bytes correctly", () => {
+    expect(formatBytes(500)).toBe("500 B");
+  });
+
+  it("formats kilobytes", () => {
+    expect(formatBytes(1024)).toBe("1.00 KB");
+    expect(formatBytes(1536)).toBe("1.50 KB");
+  });
+
+  it("formats megabytes", () => {
+    expect(formatBytes(1048576)).toBe("1.00 MB");
+    expect(formatBytes(1572864)).toBe("1.50 MB");
+  });
+
+  it("formats gigabytes", () => {
+    expect(formatBytes(1073741824)).toBe("1.00 GB");
+  });
+
+  it("formats terabytes", () => {
+    expect(formatBytes(1099511627776)).toBe("1.00 TB");
+  });
+});
+
+describe("formatEta", () => {
+  it('returns "--" for null/undefined', () => {
+    expect(formatEta(null)).toBe("--");
+    expect(formatEta(undefined)).toBe("--");
+  });
+
+  it('returns "--" for negative values', () => {
+    expect(formatEta(-5)).toBe("--");
+  });
+
+  it("formats seconds", () => {
+    expect(formatEta(30)).toBe("30s");
+    expect(formatEta(1)).toBe("1s");
+  });
+
+  it("formats minutes and seconds", () => {
+    expect(formatEta(90)).toBe("1m 30s");
+    expect(formatEta(125)).toBe("2m 5s");
+  });
+
+  it("formats hours and minutes", () => {
+    expect(formatEta(3661)).toBe("1h 1m");
+    expect(formatEta(7200)).toBe("2h 0m");
+  });
+});
+
+describe("formatDuration", () => {
+  it("formats sub-second durations as milliseconds", () => {
+    expect(formatDuration(0.5)).toBe("500ms");
+    expect(formatDuration(0.001)).toBe("1ms");
+  });
+
+  it("formats seconds with one decimal", () => {
+    expect(formatDuration(5.3)).toBe("5.3s");
+    expect(formatDuration(30.0)).toBe("30.0s");
+  });
+
+  it("formats minutes and seconds", () => {
+    expect(formatDuration(90)).toBe("1m 30s");
+    expect(formatDuration(125)).toBe("2m 5s");
+  });
+});
+
+describe("formatDate", () => {
+  it("formats a Unix epoch into a locale date string (date only)", () => {
+    // 2024-01-15 10:30:00 UTC = 1705311000
+    const result = formatDate(1705311000);
+    // Should contain date components (locale-dependent formatting)
+    expect(result).toContain("Jan");
+    expect(result).toContain("15");
+    expect(result).toContain("2024");
+    // Should NOT contain time
+    expect(result).not.toContain(":");
+  });
+});
+
+describe("formatDateTime", () => {
+  it('returns "-" for null/undefined', () => {
+    expect(formatDateTime(null)).toBe("-");
+    expect(formatDateTime(undefined)).toBe("-");
+  });
+
+  it('returns "-" for zero', () => {
+    expect(formatDateTime(0)).toBe("-");
+  });
+
+  it("formats a Unix epoch into a locale datetime string", () => {
+    // 2024-01-15 10:30:00 UTC = 1705311000
+    const result = formatDateTime(1705311000);
+    // Should contain date components (locale-dependent formatting)
+    expect(result).toContain("Jan");
+    expect(result).toContain("15");
+    expect(result).toContain("2024");
+    // Should also contain time
+    expect(result).toContain(":");
+  });
+});
diff --git a/frontend/vitest.config.ts b/frontend/vitest.config.ts
new file mode 100644
index 0000000..738362e
--- /dev/null
+++ b/frontend/vitest.config.ts
@@ -0,0 +1,12 @@
+import react from "@vitejs/plugin-react";
+import { defineConfig } from "vitest/config";
+
+export default defineConfig({
+  plugins: [react()],
+  test: {
+    globals: true,
+    environment: "jsdom",
+    setupFiles: ["./tests/setup.ts"],
+    css: true,
+  },
+});

From 8fc4c63dc995fbbe2fec34de965690a90f62b1f5 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:33:27 -0700
Subject: [PATCH 116/173] Ignore: Don't ignore nested logs dirs

---
 .gitignore          | 2 +-
 frontend/.gitignore | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 447eb83..0716996 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,7 +6,7 @@ settings.json
 modaq_upload_cache.db
 
 # Log files
-logs/
+/logs/
 
 # Python
 __pycache__/
diff --git a/frontend/.gitignore b/frontend/.gitignore
index 982baa9..be7b770 100644
--- a/frontend/.gitignore
+++ b/frontend/.gitignore
@@ -1,5 +1,5 @@
 # Logs
-logs
+/logs
 *.log
 npm-debug.log*
 yarn-debug.log*

From 74d17f79ae4ddcecf4055b9aa1d63a1aa4729508 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:35:10 -0700
Subject: [PATCH 117/173] Frontend: Add CSV Preview component

---
 frontend/src/components/logs/CsvPreview.tsx | 182 ++++++++++++++++++++
 1 file changed, 182 insertions(+)
 create mode 100644 frontend/src/components/logs/CsvPreview.tsx

diff --git a/frontend/src/components/logs/CsvPreview.tsx b/frontend/src/components/logs/CsvPreview.tsx
new file mode 100644
index 0000000..523e188
--- /dev/null
+++ b/frontend/src/components/logs/CsvPreview.tsx
@@ -0,0 +1,182 @@
+import { useCallback, useState } from "react";
+import { apiGet } from "../../api/client.ts";
+import type { CsvFileInfo, CsvPreviewResponse } from "../../types/api.ts";
+
+function formatBytes(bytes: number): string {
+  if (bytes === 0) return "0 B";
+  const units = ["B", "KB", "MB", "GB", "TB"];
+  const i = Math.floor(Math.log(bytes) / Math.log(1024));
+  return `${(bytes / 1024 ** i).toFixed(i === 0 ? 0 : 1)} ${units[i]}`;
+}
+
+interface CsvPreviewProps {
+  csvFiles: CsvFileInfo[];
+}
+
+export default function CsvPreview({ csvFiles }: CsvPreviewProps) {
+  const [expanded, setExpanded] = useState(false);
+  const [previewPath, setPreviewPath] = useState<string | null>(null);
+  const [previewData, setPreviewData] = useState<CsvPreviewResponse | null>(null);
+  const [previewLoading, setPreviewLoading] = useState(false);
+  const [previewError, setPreviewError] = useState<string | null>(null);
+
+  const loadPreview = useCallback(async (path: string) => {
+    // Toggle off if clicking same file
+    if (previewPath === path) {
+      setPreviewPath(null);
+      setPreviewData(null);
+      return;
+    }
+
+    setPreviewPath(path);
+    setPreviewLoading(true);
+    setPreviewError(null);
+    try {
+      const data = await apiGet<CsvPreviewResponse>("/api/logs/csv-preview", { path });
+      setPreviewData(data);
+    } catch (err) {
+      setPreviewError(err instanceof Error ? err.message : "Failed to load preview");
+    } finally {
+      setPreviewLoading(false);
+    }
+  }, [previewPath]);
+
+  if (csvFiles.length === 0) {
+    return null;
+  }
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200 overflow-hidden">
+      {/* Collapsible header */}
+      <button
+        onClick={() => setExpanded((prev) => !prev)}
+        className="w-full flex items-center justify-between px-4 py-3 hover:bg-gray-50 transition-colors"
+      >
+        <div className="flex items-center gap-2">
+          <svg className="h-5 w-5 text-nlr-green" fill="none" viewBox="0 0 24 24" stroke="currentColor">
+            <path
+              strokeLinecap="round"
+              strokeLinejoin="round"
+              strokeWidth={2}
+              d="M9 17v-2m3 2v-4m3 4v-6m2 10H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z"
+            />
+          </svg>
+          <span className="text-sm font-semibold text-gray-700">
+            Upload Summaries ({csvFiles.length})
+          </span>
+        </div>
+        <svg
+          className={`w-5 h-5 text-gray-400 transition-transform ${expanded ? "rotate-180" : ""}`}
+          fill="none"
+          viewBox="0 0 24 24"
+          stroke="currentColor"
+        >
+          <path
+            strokeLinecap="round"
+            strokeLinejoin="round"
+            strokeWidth={2}
+            d="M19 9l-7 7-7-7"
+          />
+        </svg>
+      </button>
+
+      {expanded && (
+        <div className="border-t border-gray-200">
+          {/* CSV file list */}
+          <div className="divide-y divide-gray-100">
+            {csvFiles.map((file) => (
+              <div key={file.path}>
+                <div className="flex items-center gap-3 px-4 py-3 hover:bg-gray-50 transition-colors">
+                  <svg
+                    className="h-4 w-4 text-gray-400 shrink-0"
+                    fill="none"
+                    viewBox="0 0 24 24"
+                    stroke="currentColor"
+                  >
+                    <path
+                      strokeLinecap="round"
+                      strokeLinejoin="round"
+                      strokeWidth={2}
+                      d="M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z"
+                    />
+                  </svg>
+                  <div className="flex-1 min-w-0">
+                    <p className="text-sm font-medium text-gray-900 truncate">{file.filename}</p>
+                    <p className="text-xs text-gray-400">
+                      {file.date} -- {formatBytes(file.size)}
+                    </p>
+                  </div>
+                  <div className="flex gap-2 shrink-0">
+                    <button
+                      onClick={() => loadPreview(file.path)}
+                      className={`px-3 py-1 text-xs rounded border transition-colors ${
+                        previewPath === file.path
+                          ? "bg-nlr-blue text-white border-nlr-blue"
+                          : "border-gray-300 text-gray-600 hover:bg-gray-100"
+                      }`}
+                    >
+                      {previewPath === file.path ? "Hide" : "View"}
+                    </button>
+                    <a
+                      href={`/api/logs/csv-download?path=${encodeURIComponent(file.path)}`}
+                      className="px-3 py-1 text-xs rounded border border-gray-300 text-gray-600 hover:bg-gray-100 transition-colors"
+                      download
+                    >
+                      Download
+                    </a>
+                  </div>
+                </div>
+
+                {/* Inline preview */}
+                {previewPath === file.path && (
+                  <div className="px-4 pb-3">
+                    {previewLoading && (
+                      <div className="text-sm text-gray-500 py-4 text-center">
+                        Loading preview...
+                      </div>
+                    )}
+                    {previewError && (
+                      <div className="text-sm text-red-600 py-4 text-center">{previewError}</div>
+                    )}
+                    {previewData && !previewLoading && (
+                      <div className="overflow-x-auto border border-gray-200 rounded">
+                        <table className="w-full text-xs">
+                          <thead className="bg-gray-50">
+                            <tr>
+                              {previewData.columns.map((col) => (
+                                <th
+                                  key={col}
+                                  className="px-3 py-2 text-left font-medium text-gray-500 uppercase whitespace-nowrap"
+                                >
+                                  {col}
+                                </th>
+                              ))}
+                            </tr>
+                          </thead>
+                          <tbody className="divide-y divide-gray-100">
+                            {previewData.rows.map((row, i) => (
+                              <tr key={i} className="hover:bg-gray-50">
+                                {previewData.columns.map((col) => (
+                                  <td
+                                    key={col}
+                                    className="px-3 py-2 text-gray-700 whitespace-nowrap"
+                                  >
+                                    {row[col] ?? ""}
+                                  </td>
+                                ))}
+                              </tr>
+                            ))}
+                          </tbody>
+                        </table>
+                      </div>
+                    )}
+                  </div>
+                )}
+              </div>
+            ))}
+          </div>
+        </div>
+      )}
+    </div>
+  );
+}

From 8669060414c8ac949df2b025e59ae50eede302e5 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:35:27 -0700
Subject: [PATCH 118/173] Frontend: Add logs filter bar component

---
 frontend/src/components/logs/FilterBar.tsx | 128 +++++++++++++++++++++
 1 file changed, 128 insertions(+)
 create mode 100644 frontend/src/components/logs/FilterBar.tsx

diff --git a/frontend/src/components/logs/FilterBar.tsx b/frontend/src/components/logs/FilterBar.tsx
new file mode 100644
index 0000000..013bfcb
--- /dev/null
+++ b/frontend/src/components/logs/FilterBar.tsx
@@ -0,0 +1,128 @@
+import { useCallback, useEffect, useState } from "react";
+import { useDebounce } from "../../hooks/useDebounce.ts";
+
+export interface LogFilters {
+  date: string;
+  level: string;
+  category: string;
+  search: string;
+}
+
+const EMPTY_FILTERS: LogFilters = {
+  date: "",
+  level: "",
+  category: "",
+  search: "",
+};
+
+const LEVELS = ["All", "INFO", "WARNING", "ERROR"] as const;
+const CATEGORIES = ["All", "upload", "analysis", "settings", "app", "sync"] as const;
+
+interface FilterBarProps {
+  onFilterChange: (filters: LogFilters) => void;
+}
+
+export default function FilterBar({ onFilterChange }: FilterBarProps) {
+  const [filters, setFilters] = useState<LogFilters>(EMPTY_FILTERS);
+  const debouncedSearch = useDebounce(filters.search, 300);
+
+  // Notify parent when any filter changes (debounced for search)
+  const { date, level, category } = filters;
+  useEffect(() => {
+    onFilterChange({ date, level, category, search: debouncedSearch });
+  }, [date, level, category, debouncedSearch, onFilterChange]);
+
+  const updateFilter = useCallback(<K extends keyof LogFilters>(key: K, value: LogFilters[K]) => {
+    setFilters((prev) => ({ ...prev, [key]: value }));
+  }, []);
+
+  const clearFilters = () => {
+    setFilters(EMPTY_FILTERS);
+  };
+
+  const hasActiveFilters =
+    filters.date !== "" || filters.level !== "" || filters.category !== "" || filters.search !== "";
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-4">
+      <div className="flex flex-wrap items-end gap-4">
+        {/* Date picker */}
+        <div className="flex flex-col gap-1">
+          <label className="text-xs font-medium text-gray-500 uppercase" htmlFor="log-date">
+            Date
+          </label>
+          <input
+            id="log-date"
+            type="date"
+            value={filters.date}
+            onChange={(e) => updateFilter("date", e.target.value)}
+            className="px-3 py-2 border border-gray-300 rounded text-sm focus:outline-none focus:ring-2 focus:ring-nlr-blue focus:border-transparent"
+          />
+        </div>
+
+        {/* Level dropdown */}
+        <div className="flex flex-col gap-1">
+          <label className="text-xs font-medium text-gray-500 uppercase" htmlFor="log-level">
+            Level
+          </label>
+          <select
+            id="log-level"
+            value={filters.level}
+            onChange={(e) => updateFilter("level", e.target.value)}
+            className="px-3 py-2 border border-gray-300 rounded text-sm focus:outline-none focus:ring-2 focus:ring-nlr-blue focus:border-transparent bg-white"
+          >
+            {LEVELS.map((level) => (
+              <option key={level} value={level === "All" ? "" : level}>
+                {level}
+              </option>
+            ))}
+          </select>
+        </div>
+
+        {/* Category dropdown */}
+        <div className="flex flex-col gap-1">
+          <label className="text-xs font-medium text-gray-500 uppercase" htmlFor="log-category">
+            Category
+          </label>
+          <select
+            id="log-category"
+            value={filters.category}
+            onChange={(e) => updateFilter("category", e.target.value)}
+            className="px-3 py-2 border border-gray-300 rounded text-sm focus:outline-none focus:ring-2 focus:ring-nlr-blue focus:border-transparent bg-white"
+          >
+            {CATEGORIES.map((cat) => (
+              <option key={cat} value={cat === "All" ? "" : cat}>
+                {cat}
+              </option>
+            ))}
+          </select>
+        </div>
+
+        {/* Search input */}
+        <div className="flex flex-col gap-1 flex-1 min-w-[200px]">
+          <label className="text-xs font-medium text-gray-500 uppercase" htmlFor="log-search">
+            Search
+          </label>
+          <input
+            id="log-search"
+            type="text"
+            value={filters.search}
+            onChange={(e) => updateFilter("search", e.target.value)}
+            placeholder="Search messages..."
+            className="px-3 py-2 border border-gray-300 rounded text-sm focus:outline-none focus:ring-2 focus:ring-nlr-blue focus:border-transparent"
+          />
+        </div>
+
+        {/* Clear button */}
+        {hasActiveFilters && (
+          <button
+            onClick={clearFilters}
+            className="px-3 py-2 text-sm text-gray-500 hover:text-gray-700 hover:bg-gray-100 rounded transition-colors"
+          >
+            Clear Filters
+          </button>
+        )}
+      </div>
+    </div>
+  );
+}

From d69e04c8df0962f161c0717e09669924cadb2430 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:35:49 -0700
Subject: [PATCH 119/173] Frontend: Add logs stats bar component

---
 frontend/src/components/logs/LogStatsBar.tsx | 72 ++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 frontend/src/components/logs/LogStatsBar.tsx

diff --git a/frontend/src/components/logs/LogStatsBar.tsx b/frontend/src/components/logs/LogStatsBar.tsx
new file mode 100644
index 0000000..a48e7c5
--- /dev/null
+++ b/frontend/src/components/logs/LogStatsBar.tsx
@@ -0,0 +1,72 @@
+import { useEffect, useState } from "react";
+import { apiGet } from "../../api/client.ts";
+import type { LogStats } from "../../types/api.ts";
+import StatCard from "../common/StatCard.tsx";
+
+interface LogStatsBarProps {
+  onStatsLoaded?: (stats: LogStats) => void;
+}
+
+export default function LogStatsBar({ onStatsLoaded }: LogStatsBarProps) {
+  const [stats, setStats] = useState<LogStats | null>(null);
+  const [error, setError] = useState<string | null>(null);
+
+  useEffect(() => {
+    async function fetchStats() {
+      try {
+        const data = await apiGet<LogStats>("/api/logs/stats");
+        setStats(data);
+        onStatsLoaded?.(data);
+      } catch (err) {
+        setError(err instanceof Error ? err.message : "Failed to load stats");
+      }
+    }
+    void fetchStats();
+  }, [onStatsLoaded]);
+
+  if (error) {
+    return (
+      <div className="text-sm text-red-600 bg-red-50 border border-red-200 rounded p-3">
+        {error}
+      </div>
+    );
+  }
+
+  if (!stats) {
+    return (
+      <div className="grid grid-cols-2 md:grid-cols-4 gap-4">
+        {Array.from({ length: 4 }).map((_, i) => (
+          <div key={i} className="bg-white rounded-lg shadow-sm border-l-4 border-gray-200 p-4 animate-pulse">
+            <div className="h-8 bg-gray-200 rounded w-16 mb-2" />
+            <div className="h-4 bg-gray-100 rounded w-24" />
+          </div>
+        ))}
+      </div>
+    );
+  }
+
+  return (
+    <div className="grid grid-cols-2 md:grid-cols-4 gap-4">
+      <StatCard
+        value={stats.total_entries.toLocaleString()}
+        label="Total Entries"
+        color="text-nlr-blue"
+      />
+      <StatCard
+        value={stats.today_entries.toLocaleString()}
+        label="Today"
+        color="text-nlr-green"
+      />
+      <StatCard
+        value={(stats.level_counts.ERROR ?? 0).toLocaleString()}
+        label="Errors"
+        color="text-red-500"
+      />
+      <StatCard
+        value={stats.file_count.toLocaleString()}
+        label="Log Files"
+        color="text-gray-600"
+      />
+    </div>
+  );
+}

From 68e6d906e666df0109cd3c830476e46e7a32334b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:36:16 -0700
Subject: [PATCH 120/173] Frontend: Add logs table component

---
 frontend/src/components/logs/LogTable.tsx | 265 ++++++++++++++++++++++
 1 file changed, 265 insertions(+)
 create mode 100644 frontend/src/components/logs/LogTable.tsx

diff --git a/frontend/src/components/logs/LogTable.tsx b/frontend/src/components/logs/LogTable.tsx
new file mode 100644
index 0000000..a9d6d50
--- /dev/null
+++ b/frontend/src/components/logs/LogTable.tsx
@@ -0,0 +1,265 @@
+import { useCallback, useEffect, useState } from "react";
+import { apiGet } from "../../api/client.ts";
+import { usePagination } from "../../hooks/usePagination.ts";
+import type { LogEntriesResponse, LogEntry } from "../../types/api.ts";
+import SortableHeader from "../common/SortableHeader.tsx";
+import type { LogFilters } from "./FilterBar.tsx";
+
+const LEVEL_BADGES: Record<string, string> = {
+  INFO: "bg-blue-100 text-blue-800",
+  WARNING: "bg-yellow-100 text-yellow-800",
+  ERROR: "bg-red-100 text-red-800",
+};
+
+function LevelBadge({ level }: { level: string }) {
+  const classes = LEVEL_BADGES[level] ?? "bg-gray-100 text-gray-800";
+  return (
+    <span className={`inline-block px-2 py-0.5 rounded text-xs font-medium ${classes}`}>
+      {level}
+    </span>
+  );
+}
+
+function formatTimestamp(iso: string): string {
+  const d = new Date(iso);
+  return d.toLocaleString(undefined, {
+    month: "short",
+    day: "numeric",
+    hour: "2-digit",
+    minute: "2-digit",
+    second: "2-digit",
+  });
+}
+
+type SortColumn = "timestamp" | "level" | "category" | "event";
+
+interface LogTableProps {
+  filters: LogFilters;
+}
+
+export default function LogTable({ filters }: LogTableProps) {
+  const [entries, setEntries] = useState<LogEntry[]>([]);
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [expandedId, setExpandedId] = useState<number | null>(null);
+  const [sortColumn, setSortColumn] = useState<SortColumn>("timestamp");
+  const [ascending, setAscending] = useState(false);
+
+  const pagination = usePagination(50);
+  const { offset, limit, setTotal, reset: paginationReset } = pagination;
+
+  const toggleSort = useCallback(
+    (column: SortColumn) => {
+      if (column === sortColumn) {
+        setAscending((prev) => !prev);
+      } else {
+        setSortColumn(column);
+        setAscending(column === "timestamp" ? false : true);
+      }
+    },
+    [sortColumn],
+  );
+
+  const fetchEntries = useCallback(async () => {
+    setLoading(true);
+    setError(null);
+    try {
+      const params: Record<string, string> = {
+        offset: String(offset),
+        limit: String(limit),
+      };
+      if (filters.date) params.date = filters.date;
+      if (filters.level) params.level = filters.level;
+      if (filters.category) params.category = filters.category;
+      if (filters.search) params.search = filters.search;
+
+      const data = await apiGet<LogEntriesResponse>("/api/logs/entries", params);
+      setEntries(data.entries);
+      setTotal(data.total);
+    } catch (err) {
+      setError(err instanceof Error ? err.message : "Failed to load log entries");
+    } finally {
+      setLoading(false);
+    }
+  }, [filters, offset, limit, setTotal]);
+
+  // Reset to page 1 when filters change
+  useEffect(() => {
+    paginationReset();
+  }, [filters.date, filters.level, filters.category, filters.search, paginationReset]);
+
+  useEffect(() => {
+    void fetchEntries();
+  }, [fetchEntries]);
+
+  // Client-side sort of the current page
+  const sortedEntries = [...entries].sort((a, b) => {
+    const aVal = a[sortColumn];
+    const bVal = b[sortColumn];
+    let cmp = 0;
+    if (typeof aVal === "string" && typeof bVal === "string") {
+      cmp = aVal.localeCompare(bVal);
+    }
+    return ascending ? cmp : -cmp;
+  });
+
+  const toggleExpand = (id: number) => {
+    setExpandedId((prev) => (prev === id ? null : id));
+  };
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200 overflow-hidden">
+      {/* Table */}
+      <div className="overflow-x-auto">
+        <table className="w-full">
+          <thead className="bg-gray-50 border-b border-gray-200">
+            <tr>
+              <SortableHeader
+                label="Timestamp"
+                active={sortColumn === "timestamp"}
+                ascending={ascending}
+                onSort={() => toggleSort("timestamp")}
+              />
+              <SortableHeader
+                label="Level"
+                active={sortColumn === "level"}
+                ascending={ascending}
+                onSort={() => toggleSort("level")}
+              />
+              <SortableHeader
+                label="Category"
+                active={sortColumn === "category"}
+                ascending={ascending}
+                onSort={() => toggleSort("category")}
+              />
+              <SortableHeader
+                label="Event"
+                active={sortColumn === "event"}
+                ascending={ascending}
+                onSort={() => toggleSort("event")}
+              />
+              <th className="px-4 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">
+                Message
+              </th>
+            </tr>
+          </thead>
+          <tbody className="divide-y divide-gray-100">
+            {loading && entries.length === 0 ? (
+              <tr>
+                <td colSpan={5} className="px-4 py-12 text-center text-sm text-gray-500">
+                  Loading log entries...
+                </td>
+              </tr>
+            ) : error ? (
+              <tr>
+                <td colSpan={5} className="px-4 py-12 text-center text-sm text-red-600">
+                  {error}
+                </td>
+              </tr>
+            ) : sortedEntries.length === 0 ? (
+              <tr>
+                <td colSpan={5} className="px-4 py-12 text-center text-sm text-gray-500">
+                  No log entries found.
+                </td>
+              </tr>
+            ) : (
+              sortedEntries.map((entry) => (
+                <LogRow
+                  key={entry.id}
+                  entry={entry}
+                  expanded={expandedId === entry.id}
+                  onToggle={() => toggleExpand(entry.id)}
+                />
+              ))
+            )}
+          </tbody>
+        </table>
+      </div>
+
+      {/* Pagination */}
+      {pagination.totalPages > 1 && (
+        <div className="flex items-center justify-between px-4 py-3 border-t border-gray-200 bg-gray-50">
+          <span className="text-sm text-gray-500">
+            Page {pagination.currentPage} of {pagination.totalPages}
+          </span>
+          <div className="flex gap-2">
+            <button
+              onClick={pagination.prevPage}
+              disabled={pagination.currentPage === 1}
+              className="px-3 py-1 text-sm border border-gray-300 rounded hover:bg-gray-100 disabled:opacity-50 disabled:cursor-not-allowed"
+            >
+              Previous
+            </button>
+            <button
+              onClick={pagination.nextPage}
+              disabled={pagination.currentPage === pagination.totalPages}
+              className="px-3 py-1 text-sm border border-gray-300 rounded hover:bg-gray-100 disabled:opacity-50 disabled:cursor-not-allowed"
+            >
+              Next
+            </button>
+          </div>
+        </div>
+      )}
+    </div>
+  );
+}
+
+/** Single log row with expandable metadata */
+function LogRow({
+  entry,
+  expanded,
+  onToggle,
+}: {
+  entry: LogEntry;
+  expanded: boolean;
+  onToggle: () => void;
+}) {
+  const hasMetadata = entry.metadata && Object.keys(entry.metadata).length > 0;
+
+  return (
+    <>
+      <tr
+        className={`hover:bg-gray-50 transition-colors ${hasMetadata ? "cursor-pointer" : ""}`}
+        onClick={hasMetadata ? onToggle : undefined}
+      >
+        <td className="px-4 py-3 text-sm text-gray-600 whitespace-nowrap">
+          {formatTimestamp(entry.timestamp)}
+        </td>
+        <td className="px-4 py-3">
+          <LevelBadge level={entry.level} />
+        </td>
+        <td className="px-4 py-3 text-sm text-gray-600">{entry.category}</td>
+        <td className="px-4 py-3 text-sm text-gray-700 font-mono text-xs">{entry.event}</td>
+        <td className="px-4 py-3 text-sm text-gray-600 max-w-md truncate" title={entry.message}>
+          <div className="flex items-center gap-2">
+            <span className="truncate">{entry.message}</span>
+            {hasMetadata && (
+              <svg
+                className={`w-4 h-4 text-gray-400 shrink-0 transition-transform ${expanded ? "rotate-180" : ""}`}
+                fill="none"
+                viewBox="0 0 24 24"
+                stroke="currentColor"
+              >
+                <path
+                  strokeLinecap="round"
+                  strokeLinejoin="round"
+                  strokeWidth={2}
+                  d="M19 9l-7 7-7-7"
+                />
+              </svg>
+            )}
+          </div>
+        </td>
+      </tr>
+      {expanded && hasMetadata && (
+        <tr>
+          <td colSpan={5} className="px-4 py-3 bg-gray-50">
+            <pre className="text-xs text-gray-700 overflow-x-auto whitespace-pre-wrap font-mono bg-white p-3 rounded border border-gray-200">
+              {JSON.stringify(entry.metadata, null, 2)}
+            </pre>
+          </td>
+        </tr>
+      )}
+    </>
+  );
+}

From 93a26a42ae4524bf64d7b9138a1bfb43b857539a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:36:31 -0700
Subject: [PATCH 121/173] Frontend: Add Upload List component

---
 .../src/components/logs/UploadSessionList.tsx | 180 ++++++++++++++++++
 1 file changed, 180 insertions(+)
 create mode 100644 frontend/src/components/logs/UploadSessionList.tsx

diff --git a/frontend/src/components/logs/UploadSessionList.tsx b/frontend/src/components/logs/UploadSessionList.tsx
new file mode 100644
index 0000000..6275f3c
--- /dev/null
+++ b/frontend/src/components/logs/UploadSessionList.tsx
@@ -0,0 +1,180 @@
+import { useState } from "react";
+import type { UploadSession, UploadSessionFile } from "../../types/api.ts";
+
+interface UploadSessionListProps {
+  sessions: UploadSession[];
+}
+
+function StatusBadge({ status }: { status: string }) {
+  const colors: Record<string, string> = {
+    completed: "bg-green-100 text-green-700",
+    skipped: "bg-gray-100 text-gray-600",
+    failed: "bg-red-100 text-red-700",
+  };
+  return (
+    <span className={`inline-block px-2 py-0.5 text-xs font-medium rounded ${colors[status] ?? "bg-gray-100 text-gray-600"}`}>
+      {status}
+    </span>
+  );
+}
+
+function SessionStatusSummary({ session }: { session: UploadSession }) {
+  const parts: { text: string; color: string }[] = [];
+  if (session.completed > 0) parts.push({ text: `${session.completed} completed`, color: "text-green-600" });
+  if (session.failed > 0) parts.push({ text: `${session.failed} failed`, color: "text-red-600" });
+  if (session.skipped > 0) parts.push({ text: `${session.skipped} skipped`, color: "text-gray-500" });
+
+  return (
+    <span className="text-sm">
+      {parts.map((p, i) => (
+        <span key={p.text}>
+          {i > 0 && <span className="text-gray-400">, </span>}
+          <span className={p.color}>{p.text}</span>
+        </span>
+      ))}
+    </span>
+  );
+}
+
+function formatDuration(seconds: number): string {
+  if (seconds < 60) return `${Math.round(seconds)}s`;
+  const m = Math.floor(seconds / 60);
+  const s = Math.round(seconds % 60);
+  return s > 0 ? `${m}m ${s}s` : `${m}m`;
+}
+
+function FileDetailTable({ files }: { files: UploadSessionFile[] }) {
+  return (
+    <div className="overflow-x-auto border border-gray-200 rounded">
+      <table className="w-full text-xs">
+        <thead className="bg-gray-50">
+          <tr>
+            <th className="px-3 py-2 text-left font-medium text-gray-500">Filename</th>
+            <th className="px-3 py-2 text-left font-medium text-gray-500">Size</th>
+            <th className="px-3 py-2 text-left font-medium text-gray-500">Status</th>
+            <th className="px-3 py-2 text-left font-medium text-gray-500">Speed</th>
+            <th className="px-3 py-2 text-left font-medium text-gray-500">S3 Path</th>
+          </tr>
+        </thead>
+        <tbody className="divide-y divide-gray-100">
+          {files.map((file) => (
+            <tr key={file.filename} className="hover:bg-gray-50">
+              <td className="px-3 py-2 text-gray-900 font-mono">{file.filename}</td>
+              <td className="px-3 py-2 text-gray-600 whitespace-nowrap">{file.file_size_formatted}</td>
+              <td className="px-3 py-2"><StatusBadge status={file.status} /></td>
+              <td className="px-3 py-2 text-gray-600 whitespace-nowrap">
+                {file.upload_speed_mbps ? `${file.upload_speed_mbps} Mbps` : "-"}
+              </td>
+              <td className="px-3 py-2 text-gray-500 font-mono text-[11px] max-w-xs truncate" title={file.s3_path}>
+                {file.s3_path || "-"}
+              </td>
+            </tr>
+          ))}
+          {/* Show error rows separately for failed files */}
+          {files
+            .filter((f) => f.status === "failed" && f.error_message)
+            .map((f) => (
+              <tr key={`${f.filename}-error`} className="bg-red-50">
+                <td colSpan={5} className="px-3 py-1.5 text-xs text-red-600">
+                  {f.filename}: {f.error_message}
+                </td>
+              </tr>
+            ))}
+        </tbody>
+      </table>
+    </div>
+  );
+}
+
+export default function UploadSessionList({ sessions }: UploadSessionListProps) {
+  const [expandedIndex, setExpandedIndex] = useState<number | null>(null);
+
+  if (sessions.length === 0) {
+    return (
+      <div className="bg-white rounded-lg border border-gray-200 p-8 text-center text-gray-500">
+        No upload sessions found. Upload some files to see history here.
+      </div>
+    );
+  }
+
+  return (
+    <div className="space-y-3">
+      {sessions.map((session, i) => {
+        const isExpanded = expandedIndex === i;
+        return (
+          <div
+            key={session.csv_path}
+            className="bg-white rounded-lg border border-gray-200 overflow-hidden"
+          >
+            {/* Session header row */}
+            <button
+              onClick={() => setExpandedIndex(isExpanded ? null : i)}
+              className="w-full flex items-center gap-4 px-4 py-3 hover:bg-gray-50 transition-colors text-left"
+            >
+              {/* Chevron */}
+              <svg
+                className={`w-4 h-4 text-gray-400 shrink-0 transition-transform ${isExpanded ? "rotate-90" : ""}`}
+                fill="none"
+                viewBox="0 0 24 24"
+                stroke="currentColor"
+              >
+                <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2} d="M9 5l7 7-7 7" />
+              </svg>
+
+              {/* Date + time */}
+              <div className="min-w-[120px]">
+                <div className="text-sm font-medium text-gray-900">{session.date}</div>
+                <div className="text-xs text-gray-400">{session.time}</div>
+              </div>
+
+              {/* File count */}
+              <div className="min-w-[80px]">
+                <div className="text-sm text-gray-700">{session.total_files} files</div>
+              </div>
+
+              {/* Total size */}
+              <div className="min-w-[80px]">
+                <div className="text-sm text-gray-700">{session.total_bytes_formatted}</div>
+              </div>
+
+              {/* Status summary */}
+              <div className="flex-1">
+                <SessionStatusSummary session={session} />
+              </div>
+
+              {/* Duration + speed */}
+              <div className="text-right shrink-0 min-w-[100px]">
+                <div className="text-xs text-gray-500">
+                  {session.total_duration_seconds > 0
+                    ? formatDuration(session.total_duration_seconds)
+                    : "-"}
+                </div>
+                <div className="text-xs text-gray-400">
+                  {session.avg_speed_mbps > 0 ? `${session.avg_speed_mbps} Mbps` : ""}
+                </div>
+              </div>
+
+              {/* Download link — stop propagation so clicking doesn't toggle expand */}
+              <a
+                href={`/api/logs/csv-download?path=${encodeURIComponent(session.csv_path)}`}
+                download
+                onClick={(e) => e.stopPropagation()}
+                className="shrink-0 px-2 py-1 text-xs rounded border border-gray-300 text-gray-600 hover:bg-gray-100 transition-colors"
+                title="Download CSV"
+              >
+                CSV
+              </a>
+            </button>
+
+            {/* Expanded file detail */}
+            {isExpanded && (
+              <div className="border-t border-gray-200 px-4 py-3">
+                <FileDetailTable files={session.files} />
+              </div>
+            )}
+          </div>
+        );
+      })}
+    </div>
+  );
+}

From 877ea27a7646489334bbccdd4f3f628d1e8b51e2 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:36:49 -0700
Subject: [PATCH 122/173] Frontend: Add upload stats bar

---
 .../src/components/logs/UploadStatsBar.tsx    | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 frontend/src/components/logs/UploadStatsBar.tsx

diff --git a/frontend/src/components/logs/UploadStatsBar.tsx b/frontend/src/components/logs/UploadStatsBar.tsx
new file mode 100644
index 0000000..1b434c1
--- /dev/null
+++ b/frontend/src/components/logs/UploadStatsBar.tsx
@@ -0,0 +1,72 @@
+import { useEffect, useState } from "react";
+import { apiGet } from "../../api/client.ts";
+import type { UploadStatsResponse } from "../../types/api.ts";
+import StatCard from "../common/StatCard.tsx";
+
+interface UploadStatsBarProps {
+  onDataLoaded?: (data: UploadStatsResponse) => void;
+}
+
+export default function UploadStatsBar({ onDataLoaded }: UploadStatsBarProps) {
+  const [stats, setStats] = useState<UploadStatsResponse | null>(null);
+  const [error, setError] = useState<string | null>(null);
+
+  useEffect(() => {
+    async function fetchStats() {
+      try {
+        const data = await apiGet<UploadStatsResponse>("/api/logs/upload-stats");
+        setStats(data);
+        onDataLoaded?.(data);
+      } catch (err) {
+        setError(err instanceof Error ? err.message : "Failed to load upload stats");
+      }
+    }
+    void fetchStats();
+  }, [onDataLoaded]);
+
+  if (error) {
+    return (
+      <div className="text-sm text-red-600 bg-red-50 border border-red-200 rounded p-3">
+        {error}
+      </div>
+    );
+  }
+
+  if (!stats) {
+    return (
+      <div className="grid grid-cols-2 md:grid-cols-4 gap-4">
+        {Array.from({ length: 4 }).map((_, i) => (
+          <div key={i} className="bg-white rounded-lg shadow-sm border-l-4 border-gray-200 p-4 animate-pulse">
+            <div className="h-8 bg-gray-200 rounded w-16 mb-2" />
+            <div className="h-4 bg-gray-100 rounded w-24" />
+          </div>
+        ))}
+      </div>
+    );
+  }
+
+  return (
+    <div className="grid grid-cols-2 md:grid-cols-4 gap-4">
+      <StatCard
+        value={stats.total_files_uploaded.toLocaleString()}
+        label="Files Uploaded"
+        color="text-nlr-blue"
+      />
+      <StatCard
+        value={stats.total_bytes_uploaded_formatted}
+        label="Data Uploaded"
+        color="text-nlr-green"
+      />
+      <StatCard
+        value={stats.total_files_failed.toLocaleString()}
+        label="Failed"
+        color="text-red-500"
+      />
+      <StatCard
+        value={stats.total_sessions.toLocaleString()}
+        label="Upload Sessions"
+        color="text-gray-600"
+      />
+    </div>
+  );
+}

From df4e0741987af24453d6ed90a60ae58a2e783538 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:45:28 -0700
Subject: [PATCH 123/173] Backend: Use os.walk for error tolerant file tree
 walking

---
 app/routes/files.py | 38 +++++++++++++++++++++++---------------
 1 file changed, 23 insertions(+), 15 deletions(-)

diff --git a/app/routes/files.py b/app/routes/files.py
index 61b9d78..f7efeef 100644
--- a/app/routes/files.py
+++ b/app/routes/files.py
@@ -1,5 +1,6 @@
 """File browsing API routes for modaq_upload"""
 
+import os
 from pathlib import Path
 
 from flask import Blueprint, Response, g, jsonify, request
@@ -142,7 +143,9 @@ def browse_local() -> tuple[Response, int]:
     if not path.is_dir():
         return jsonify({"error": f"Not a directory: {path}"}), 400
 
-    # Build response — single-pass rglob for recursive MCAP counts + cache checks
+    # Build response — single-pass walk for recursive MCAP counts + cache checks.
+    # os.walk with onerror skips unreadable subdirectories instead of aborting,
+    # which is important on Linux where permission errors are common.
     cache = get_cache_service()
     bucket = g.settings.s3_bucket
 
@@ -152,23 +155,30 @@ def browse_local() -> tuple[Response, int]:
     mcap_count = 0
     direct_uploaded = 0
 
-    try:
-        for mcap_path in path.rglob("*.mcap"):
-            # Skip hidden paths (any component starting with .)
-            if any(part.startswith(".") for part in mcap_path.relative_to(path).parts):
+    def _walk_error(err: OSError) -> None:
+        pass  # Skip unreadable directories silently
+
+    for dirpath, dirnames, filenames in os.walk(str(path), onerror=_walk_error):
+        # Skip hidden directories in-place so os.walk won't descend into them
+        dirnames[:] = [d for d in dirnames if not d.startswith(".")]
+
+        for fname in filenames:
+            if not fname.endswith(".mcap") or fname.startswith("."):
                 continue
 
-            # Check cache for already-uploaded status
+            mcap_path = Path(dirpath) / fname
+            rel = mcap_path.relative_to(path)
+            parts = rel.parts
+
             try:
                 file_stat = mcap_path.stat()
-                uploaded = cache.check_exists_by_filename(
-                    bucket, mcap_path.name, file_stat.st_size
-                ) is True
-            except PermissionError:
+            except OSError:
                 continue
 
-            rel = mcap_path.relative_to(path)
-            parts = rel.parts
+            uploaded = cache.check_exists_by_filename(
+                bucket, mcap_path.name, file_stat.st_size
+            ) is True
+
             if len(parts) == 1:
                 # Direct child MCAP file
                 mcap_count += 1
@@ -191,8 +201,6 @@ def browse_local() -> tuple[Response, int]:
                     folder_uploaded_counts[folder_name] = (
                         folder_uploaded_counts.get(folder_name, 0) + 1
                     )
-    except PermissionError:
-        return jsonify({"error": f"Permission denied: {path}"}), 403
 
     # Build folder list from direct children (non-hidden directories)
     folders: list[dict[str, str | int]] = []
@@ -237,7 +245,7 @@ def browse_local() -> tuple[Response, int]:
     volumes_path = Path("/Volumes")
     if volumes_path.exists():
         try:
-            for vol in volumes_path.iterdir():
+            for vol in sorted(volumes_path.iterdir(), key=lambda x: x.name.lower()):
                 if vol.is_dir() and not vol.name.startswith("."):
                     quick_links.append({"name": vol.name, "path": str(vol)})
         except PermissionError:

From 270b5fda562a6763c1b0a53f149b4efe1b2c79eb Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 10:45:54 -0700
Subject: [PATCH 124/173] Backend: Add /media/m2 and /media to preset paths

---
 app/routes/files.py | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/app/routes/files.py b/app/routes/files.py
index f7efeef..067e784 100644
--- a/app/routes/files.py
+++ b/app/routes/files.py
@@ -251,6 +251,40 @@ def _walk_error(err: OSError) -> None:
         except PermissionError:
             pass
 
+    # Add /media/m2 as a priority quick link on Linux if it exists
+    media_m2 = Path("/media/m2")
+    if media_m2.exists() and media_m2.is_dir():
+        quick_links.append({"name": "m2", "path": str(media_m2)})
+
+    # Add /media itself and its subdirectories on Linux (removable drives, USB, etc.)
+    media_path = Path("/media")
+    if media_path.exists() and not volumes_path.exists():
+        quick_links.append({"name": "media", "path": str(media_path)})
+        try:
+            for entry in sorted(media_path.iterdir(), key=lambda x: x.name.lower()):
+                if not entry.is_dir() or entry.name.startswith("."):
+                    continue
+                entry_str = str(entry)
+                # Already added /media/m2 above
+                if entry_str == str(media_m2):
+                    continue
+                # If it's a user directory (e.g. /media/username), list its children
+                try:
+                    children = [
+                        c
+                        for c in entry.iterdir()
+                        if c.is_dir() and not c.name.startswith(".")
+                    ]
+                except PermissionError:
+                    children = []
+                if children:
+                    for child in sorted(children, key=lambda x: x.name.lower()):
+                        quick_links.append({"name": child.name, "path": str(child)})
+                else:
+                    quick_links.append({"name": entry.name, "path": entry_str})
+        except PermissionError:
+            pass
+
     return jsonify(
         {
             "success": True,

From 1b63c27db808fe37cda2fa3e1f98ef3403952c20 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 11:31:14 -0700
Subject: [PATCH 125/173] Refactor: Validate and upload file by file

---
 app/routes/upload.py               |  73 ++---
 app/services/upload_manager.py     | 502 +++++++++++++++++++++++++----
 frontend/src/hooks/useUploadJob.ts |   7 +-
 3 files changed, 479 insertions(+), 103 deletions(-)

diff --git a/app/routes/upload.py b/app/routes/upload.py
index f736be9..e93daa4 100644
--- a/app/routes/upload.py
+++ b/app/routes/upload.py
@@ -483,10 +483,12 @@ def run_scan() -> None:
     thread = threading.Thread(target=run_scan, daemon=True)
     thread.start()
 
-    return jsonify({
-        "job_id": scan_job.job_id,
-        "status": "scanning",
-    }), 202
+    return jsonify(
+        {
+            "job_id": scan_job.job_id,
+            "status": "scanning",
+        }
+    ), 202
 
 
 @upload_bp.route("/bulk-analyze", methods=["POST"])
@@ -551,50 +553,41 @@ def upload_progress_callback(job: UploadJob) -> None:
         else:
             send_sse_event(job.job_id, job.to_progress_dict())
 
-    # Start analysis in background thread
-    def run_bulk_analysis() -> None:
-        manager.analyze_job_async(
-            job.job_id,
-            settings.aws_profile,
-            settings.aws_region,
-            settings.s3_bucket,
-            progress_callback=analysis_progress_callback,
-        )
-
-        # Send analysis complete event
-        final_job = manager.get_job(job.job_id)
-        if final_job:
-            send_sse_event(
+    # Start in background thread
+    def run_bulk_job() -> None:
+        if auto_upload:
+            # Pipeline: analyze each file and upload immediately as it's ready.
+            # Uploads start flowing while remaining files are still being parsed.
+            manager.analyze_and_upload_pipeline(
                 job.job_id,
-                {
-                    "type": "analysis_complete",
-                    "job": final_job.to_dict(),
-                    "auto_upload": final_job.auto_upload,
-                },
+                settings.aws_profile,
+                settings.aws_region,
+                settings.s3_bucket,
+                skip_duplicates=skip_duplicates,
+                analysis_callback=analysis_progress_callback,
+                upload_callback=upload_progress_callback,
             )
-
-            # Auto-upload if enabled and analysis succeeded
-            if final_job.auto_upload and final_job.status == UploadStatus.READY:
+        else:
+            # Analysis only — user will review results before starting upload.
+            manager.analyze_job_async(
+                job.job_id,
+                settings.aws_profile,
+                settings.aws_region,
+                settings.s3_bucket,
+                progress_callback=analysis_progress_callback,
+            )
+            final_job = manager.get_job(job.job_id)
+            if final_job:
                 send_sse_event(
                     job.job_id,
                     {
-                        "type": "auto_upload_starting",
-                        "job_id": job.job_id,
+                        "type": "analysis_complete",
+                        "job": final_job.to_dict(),
+                        "auto_upload": False,
                     },
                 )
-                manager.start_upload(
-                    job.job_id,
-                    settings.aws_profile,
-                    settings.aws_region,
-                    settings.s3_bucket,
-                    skip_duplicates=skip_duplicates,
-                    progress_callback=upload_progress_callback,
-                )
-            elif final_job.auto_upload:
-                # All files failed analysis — send terminal status so frontend doesn't hang
-                send_sse_event(job.job_id, final_job.to_dict())
 
-    thread = threading.Thread(target=run_bulk_analysis, daemon=True)
+    thread = threading.Thread(target=run_bulk_job, daemon=True)
     thread.start()
 
     return jsonify(
diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index 0057666..b98eb0a 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -442,9 +442,7 @@ def _check_duplicate(
         if cache_result is not None:
             file_state.is_duplicate = cache_result
         else:
-            file_state.is_duplicate = s3_service.check_file_exists(
-                s3_client, s3_bucket, s3_path
-            )
+            file_state.is_duplicate = s3_service.check_file_exists(s3_client, s3_bucket, s3_path)
             if use_cache:
                 cache = get_cache_service()
                 cache.update_cache(
@@ -606,9 +604,7 @@ def analyze_job_async(
 
         with ProcessPoolExecutor(max_workers=cpu_workers) as proc_executor:
             parse_futures = {
-                proc_executor.submit(
-                    _extract_start_time_worker, file_state.local_path
-                ): file_state
+                proc_executor.submit(_extract_start_time_worker, file_state.local_path): file_state
                 for file_state in job.files
             }
             for future in as_completed(parse_futures):
@@ -931,9 +927,357 @@ def byte_callback(uploaded: int, total: int) -> None:
         # Save per-job JSONL summary
         try:
             completed_at = job.completed_at or datetime.now(UTC)
-            log.save_job_jsonl(job_id, {
-                "timestamp": completed_at.isoformat(),
-                "event": "upload_job_completed",
+            log.save_job_jsonl(
+                job_id,
+                {
+                    "timestamp": completed_at.isoformat(),
+                    "event": "upload_job_completed",
+                    "job_id": job_id,
+                    "status": job.status.value,
+                    "uploaded": uploaded_count,
+                    "skipped": skipped_count,
+                    "failed": failed_count,
+                    "total_bytes_uploaded": job.successfully_uploaded_bytes,
+                    "duration_seconds": job.total_upload_duration_seconds,
+                    "avg_speed_mbps": job.average_upload_speed_mbps,
+                    "files": file_summary,
+                },
+                completed_at,
+            )
+        except Exception:
+            logger.warning("Failed to save job JSONL summary", exc_info=True)
+
+        # Save upload summary CSV
+        try:
+            log.save_job_csv(job_id, job, completed_at)
+        except Exception:
+            logger.warning("Failed to save job CSV summary", exc_info=True)
+
+        # Auto-sync logs to S3 after job completion
+        try:
+            log.sync_logs_to_s3(s3_client, s3_bucket)
+        except Exception:
+            logger.debug("Log sync to S3 failed", exc_info=True)
+
+        if progress_callback:
+            progress_callback(job)
+
+    def analyze_and_upload_pipeline(
+        self,
+        job_id: str,
+        aws_profile: str,
+        aws_region: str,
+        s3_bucket: str,
+        skip_duplicates: bool = True,
+        analysis_callback: Callable[["UploadJob", FileUploadState], None] | None = None,
+        upload_callback: Callable[["UploadJob"], None] | None = None,
+        use_cache: bool = True,
+    ) -> None:
+        """Analyze each file and upload it immediately — pipeline approach.
+
+        Instead of analyzing all files first and then uploading, this processes
+        files through a pipeline: MCAP parsing runs in a ProcessPoolExecutor,
+        and as each parse completes the file is immediately checked for duplicates
+        and submitted to a ThreadPoolExecutor for upload.
+
+        Args:
+            job_id: The job ID to process
+            aws_profile: AWS profile to use
+            aws_region: AWS region
+            s3_bucket: S3 bucket to upload to
+            skip_duplicates: Whether to skip files that already exist
+            analysis_callback: Called after each file is analyzed
+            upload_callback: Called for upload progress updates
+            use_cache: Whether to use cache for duplicate checking
+        """
+        log = get_log_service()
+        job = self.get_job(job_id)
+        if not job:
+            return
+
+        job.status = UploadStatus.UPLOADING
+        job.started_at = datetime.now(UTC)
+
+        log.info(
+            "upload",
+            "pipeline_started",
+            f"Starting analyze-and-upload pipeline for {len(job.files)} files",
+            {"job_id": job_id, "total_files": len(job.files)},
+        )
+
+        # Create S3 client
+        try:
+            s3_client = s3_service.create_s3_client(aws_profile, aws_region)
+        except Exception as e:
+            job.status = UploadStatus.FAILED
+            for file_state in job.files:
+                file_state.status = UploadStatus.FAILED
+                file_state.error_message = f"Failed to create S3 client: {e}"
+                if analysis_callback:
+                    analysis_callback(job, file_state)
+            if upload_callback:
+                upload_callback(job)
+            return
+
+        cpu_workers = max(1, (os.cpu_count() or 4) - 1)
+        upload_executor = ThreadPoolExecutor(max_workers=self.max_workers)
+
+        # Set all files to ANALYZING
+        for fs in job.files:
+            fs.status = UploadStatus.ANALYZING
+
+        try:
+            # Submit all files for MCAP parsing (CPU-bound, true parallelism)
+            with ProcessPoolExecutor(max_workers=cpu_workers) as proc_executor:
+                parse_futures = {
+                    proc_executor.submit(_extract_start_time_worker, fs.local_path): fs
+                    for fs in job.files
+                }
+
+                for future in as_completed(parse_futures):
+                    if job.cancelled:
+                        break
+
+                    fs = parse_futures[future]
+                    result = future.result()
+
+                    if isinstance(result, str):
+                        # Parse failed
+                        fs.status = UploadStatus.FAILED
+                        fs.error_message = result
+                        log.error(
+                            "analysis",
+                            "file_analysis_failed",
+                            f"Failed to analyze {fs.filename}: {result}",
+                            {"job_id": job_id, "filename": fs.filename, "error": result},
+                        )
+                        if analysis_callback:
+                            analysis_callback(job, fs)
+                        continue
+
+                    # Parse succeeded — set timestamp and generate S3 path
+                    fs.start_time = result
+                    naive_start = mcap_service.to_naive_utc(result)
+                    fs.is_valid = naive_start >= EPOCH_CUTOFF.replace(tzinfo=None)
+                    fs.s3_path = mcap_service.generate_s3_path(result, fs.filename)
+
+                    # Check duplicate (I/O but fast — cache lookup or S3 HEAD)
+                    self._check_duplicate(fs, s3_client, s3_bucket, use_cache)
+                    fs.status = UploadStatus.READY
+
+                    log.info(
+                        "analysis",
+                        "file_analysis_completed",
+                        f"Analyzed {fs.filename}",
+                        {
+                            "job_id": job_id,
+                            "filename": fs.filename,
+                            "file_size": fs.file_size,
+                            "s3_path": fs.s3_path,
+                            "is_duplicate": fs.is_duplicate,
+                            "is_valid": fs.is_valid,
+                        },
+                    )
+
+                    # Notify frontend of analysis result
+                    if analysis_callback:
+                        analysis_callback(job, fs)
+
+                    # Decide: skip or upload?
+                    if not fs.is_valid:
+                        fs.status = UploadStatus.SKIPPED
+                        fs.error_message = "Invalid timestamp (pre-1980)"
+                        log.warning(
+                            "upload",
+                            "file_upload_skipped",
+                            f"Skipped invalid timestamp: {fs.filename}",
+                            {
+                                "job_id": job_id,
+                                "filename": fs.filename,
+                                "reason": "invalid_timestamp",
+                            },
+                        )
+                        if upload_callback:
+                            upload_callback(job)
+                        continue
+
+                    if skip_duplicates and fs.is_duplicate:
+                        fs.status = UploadStatus.SKIPPED
+                        fs.bytes_uploaded = fs.file_size
+                        log.info(
+                            "upload",
+                            "file_upload_skipped",
+                            f"Skipped duplicate: {fs.filename}",
+                            {
+                                "job_id": job_id,
+                                "filename": fs.filename,
+                                "reason": "duplicate",
+                            },
+                        )
+                        if upload_callback:
+                            upload_callback(job)
+                        continue
+
+                    # Submit for upload immediately
+                    def make_upload_task(
+                        file_state: FileUploadState,
+                    ) -> Callable[[], Any]:
+                        def upload_task() -> Any:
+                            if job.cancelled:
+                                with job.lock:
+                                    file_state.status = UploadStatus.CANCELLED
+                                return None
+
+                            try:
+                                with job.lock:
+                                    file_state.status = UploadStatus.UPLOADING
+                                    file_state.upload_started_at = datetime.now(UTC)
+                                log.info(
+                                    "upload",
+                                    "file_upload_started",
+                                    f"Uploading {file_state.filename}",
+                                    {
+                                        "job_id": job_id,
+                                        "filename": file_state.filename,
+                                        "file_size": file_state.file_size,
+                                        "s3_path": file_state.s3_path,
+                                    },
+                                )
+                                if upload_callback:
+                                    upload_callback(job)
+
+                                def byte_callback(uploaded: int, total: int) -> None:
+                                    with job.lock:
+                                        file_state.bytes_uploaded = uploaded
+                                    if upload_callback:
+                                        upload_callback(job)
+
+                                upload_result = s3_service.upload_file_with_progress(
+                                    s3_client,
+                                    file_state.local_path,
+                                    s3_bucket,
+                                    file_state.s3_path,
+                                    byte_callback,
+                                )
+
+                                # Handle completion inline
+                                file_state.upload_completed_at = datetime.now(UTC)
+                                if upload_result["success"]:
+                                    file_state.status = UploadStatus.COMPLETED
+                                    file_state.bytes_uploaded = file_state.file_size
+                                    log.info(
+                                        "upload",
+                                        "file_upload_completed",
+                                        f"Uploaded {file_state.filename}",
+                                        {
+                                            "job_id": job_id,
+                                            "filename": file_state.filename,
+                                            "file_size": file_state.file_size,
+                                            "upload_duration_seconds": (
+                                                file_state.upload_duration_seconds
+                                            ),
+                                            "s3_path": file_state.s3_path,
+                                        },
+                                    )
+                                    try:
+                                        cache = get_cache_service()
+                                        cache.update_cache(
+                                            s3_bucket,
+                                            file_state.s3_path,
+                                            exists=True,
+                                            filename=file_state.filename,
+                                            file_size=file_state.file_size,
+                                        )
+                                    except Exception:
+                                        logger.debug(
+                                            "Cache update failed after upload",
+                                            exc_info=True,
+                                        )
+                                else:
+                                    file_state.status = UploadStatus.FAILED
+                                    file_state.error_message = upload_result.get(
+                                        "error", "Unknown error"
+                                    )
+                                    log.error(
+                                        "upload",
+                                        "file_upload_failed",
+                                        f"Failed to upload {file_state.filename}: "
+                                        f"{file_state.error_message}",
+                                        {
+                                            "job_id": job_id,
+                                            "filename": file_state.filename,
+                                            "error": file_state.error_message,
+                                        },
+                                    )
+                            except Exception as e:
+                                file_state.upload_completed_at = datetime.now(UTC)
+                                file_state.status = UploadStatus.FAILED
+                                file_state.error_message = str(e)
+                                log.error(
+                                    "upload",
+                                    "file_upload_failed",
+                                    f"Failed to upload {file_state.filename}: {e}",
+                                    {
+                                        "job_id": job_id,
+                                        "filename": file_state.filename,
+                                        "error": str(e),
+                                    },
+                                )
+
+                            if upload_callback:
+                                upload_callback(job)
+                            return None
+
+                        return upload_task
+
+                    upload_executor.submit(make_upload_task(fs))
+
+        except Exception as e:
+            log.error(
+                "upload",
+                "pipeline_error",
+                f"Pipeline error: {e}",
+                {"job_id": job_id, "error": str(e)},
+            )
+        finally:
+            # Wait for all in-flight uploads to complete
+            upload_executor.shutdown(wait=True)
+
+        # Final job status
+        job.completed_at = datetime.now(UTC)
+        if job.cancelled:
+            job.status = UploadStatus.CANCELLED
+        elif all(f.status in (UploadStatus.COMPLETED, UploadStatus.SKIPPED) for f in job.files):
+            job.status = UploadStatus.COMPLETED
+        elif any(f.status == UploadStatus.COMPLETED for f in job.files):
+            job.status = UploadStatus.COMPLETED  # Partial success
+        else:
+            job.status = UploadStatus.FAILED
+
+        # Clean up temp directory
+        self.cleanup_temp_dir(job_id)
+
+        uploaded_count = sum(1 for f in job.files if f.status == UploadStatus.COMPLETED)
+        skipped_count = sum(1 for f in job.files if f.status == UploadStatus.SKIPPED)
+        failed_count = sum(1 for f in job.files if f.status == UploadStatus.FAILED)
+
+        file_summary = [
+            {
+                "filename": f.filename,
+                "s3_path": f.s3_path,
+                "status": f.status.value,
+                "file_size": f.file_size,
+                "duration_seconds": f.upload_duration_seconds,
+            }
+            for f in job.files
+        ]
+
+        log.info(
+            "upload",
+            "upload_job_completed",
+            f"Upload job completed: {uploaded_count} uploaded, "
+            f"{skipped_count} skipped, {failed_count} failed",
+            {
                 "job_id": job_id,
                 "status": job.status.value,
                 "uploaded": uploaded_count,
@@ -943,7 +1287,29 @@ def byte_callback(uploaded: int, total: int) -> None:
                 "duration_seconds": job.total_upload_duration_seconds,
                 "avg_speed_mbps": job.average_upload_speed_mbps,
                 "files": file_summary,
-            }, completed_at)
+            },
+        )
+
+        # Save per-job JSONL summary
+        completed_at = job.completed_at or datetime.now(UTC)
+        try:
+            log.save_job_jsonl(
+                job_id,
+                {
+                    "timestamp": completed_at.isoformat(),
+                    "event": "upload_job_completed",
+                    "job_id": job_id,
+                    "status": job.status.value,
+                    "uploaded": uploaded_count,
+                    "skipped": skipped_count,
+                    "failed": failed_count,
+                    "total_bytes_uploaded": job.successfully_uploaded_bytes,
+                    "duration_seconds": job.total_upload_duration_seconds,
+                    "avg_speed_mbps": job.average_upload_speed_mbps,
+                    "files": file_summary,
+                },
+                completed_at,
+            )
         except Exception:
             logger.warning("Failed to save job JSONL summary", exc_info=True)
 
@@ -953,14 +1319,14 @@ def byte_callback(uploaded: int, total: int) -> None:
         except Exception:
             logger.warning("Failed to save job CSV summary", exc_info=True)
 
-        # Auto-sync logs to S3 after job completion
+        # Auto-sync logs to S3
         try:
             log.sync_logs_to_s3(s3_client, s3_bucket)
         except Exception:
             logger.debug("Log sync to S3 failed", exc_info=True)
 
-        if progress_callback:
-            progress_callback(job)
+        if upload_callback:
+            upload_callback(job)
 
     def cancel_job(self, job_id: str) -> bool:
         """Cancel an upload job.
@@ -1071,9 +1437,7 @@ def pre_filter_files(
             }
 
             # First: check cache by filename+size (works regardless of timestamp source)
-            filename_result = cache.check_exists_by_filename(
-                s3_bucket, path.name, stat.st_size
-            )
+            filename_result = cache.check_exists_by_filename(s3_bucket, path.name, stat.st_size)
             if filename_result is True:
                 stats["cache_hits"] += 1
                 stats["cache_skipped"] += 1
@@ -1135,9 +1499,7 @@ def check_s3(s3_path: str) -> bool:
                     ):
                         # Update cache with result
                         fs = file_statuses[idx]
-                        cache.update_cache(
-                            s3_bucket, s3_path, exists, fs["filename"], fs["size"]
-                        )
+                        cache.update_cache(s3_bucket, s3_path, exists, fs["filename"], fs["size"])
                         if exists:
                             stats["s3_hits"] += 1
                             fs["already_uploaded"] = True
@@ -1250,20 +1612,26 @@ def scan_folder_async(
 
             if scan_job.cancelled:
                 if progress_callback:
-                    progress_callback(job_id, {
-                        "type": "scan_complete",
-                        "status": "cancelled",
-                    })
+                    progress_callback(
+                        job_id,
+                        {
+                            "type": "scan_complete",
+                            "status": "cancelled",
+                        },
+                    )
                 return
 
             scan_job.folders_total = len(folder_map)
 
             if progress_callback:
-                progress_callback(job_id, {
-                    "type": "scan_started",
-                    "folders_total": scan_job.folders_total,
-                    "root_folder": scan_job.root_folder,
-                })
+                progress_callback(
+                    job_id,
+                    {
+                        "type": "scan_started",
+                        "folders_total": scan_job.folders_total,
+                        "root_folder": scan_job.root_folder,
+                    },
+                )
 
             # Phase 2: Process each subfolder
             for folder_path_str, mcap_paths in sorted(folder_map.items()):
@@ -1283,17 +1651,22 @@ def scan_folder_async(
                         stat = mcap_path.stat()
                         file_paths.append(str(mcap_path))
                         folder_size += stat.st_size
-                        files_info.append({
-                            "path": str(mcap_path),
-                            "filename": mcap_path.name,
-                            "size": stat.st_size,
-                            "mtime": stat.st_mtime,
-                            "relative_path": str(mcap_path.relative_to(root)),
-                        })
+                        files_info.append(
+                            {
+                                "path": str(mcap_path),
+                                "filename": mcap_path.name,
+                                "size": stat.st_size,
+                                "mtime": stat.st_mtime,
+                                "relative_path": str(mcap_path.relative_to(root)),
+                            }
+                        )
 
                     # Pre-filter this batch for duplicates
                     _, pre_stats = self.pre_filter_files(
-                        file_paths, s3_bucket, aws_profile, aws_region,
+                        file_paths,
+                        s3_bucket,
+                        aws_profile,
+                        aws_region,
                         cache_only=cache_only,
                     )
 
@@ -1353,17 +1726,20 @@ def scan_folder_async(
                     scan_job.scanned_folders.append(folder_dict)
 
                 if progress_callback:
-                    progress_callback(job_id, {
-                        "type": "scan_folder_complete",
-                        "folder": folder_dict,
-                        "folders_scanned": scan_job.folders_scanned,
-                        "folders_total": scan_job.folders_total,
-                        "running_totals": {
-                            "total_files_found": scan_job.total_files_found,
-                            "total_already_uploaded": scan_job.total_already_uploaded,
-                            "total_size": scan_job.total_size,
+                    progress_callback(
+                        job_id,
+                        {
+                            "type": "scan_folder_complete",
+                            "folder": folder_dict,
+                            "folders_scanned": scan_job.folders_scanned,
+                            "folders_total": scan_job.folders_total,
+                            "running_totals": {
+                                "total_files_found": scan_job.total_files_found,
+                                "total_already_uploaded": scan_job.total_already_uploaded,
+                                "total_size": scan_job.total_size,
+                            },
                         },
-                    })
+                    )
 
             # Terminal event
             with scan_job.lock:
@@ -1373,15 +1749,18 @@ def scan_folder_async(
                     scan_job.status = "completed"
 
             if progress_callback:
-                progress_callback(job_id, {
-                    "type": "scan_complete",
-                    "status": scan_job.status,
-                    "folders_scanned": scan_job.folders_scanned,
-                    "folders_total": scan_job.folders_total,
-                    "total_files_found": scan_job.total_files_found,
-                    "total_already_uploaded": scan_job.total_already_uploaded,
-                    "total_size": scan_job.total_size,
-                })
+                progress_callback(
+                    job_id,
+                    {
+                        "type": "scan_complete",
+                        "status": scan_job.status,
+                        "folders_scanned": scan_job.folders_scanned,
+                        "folders_total": scan_job.folders_total,
+                        "total_files_found": scan_job.total_files_found,
+                        "total_already_uploaded": scan_job.total_already_uploaded,
+                        "total_size": scan_job.total_size,
+                    },
+                )
 
         except Exception as e:
             scan_job.status = "failed"
@@ -1392,11 +1771,14 @@ def scan_folder_async(
                 {"job_id": job_id, "error": str(e)},
             )
             if progress_callback:
-                progress_callback(job_id, {
-                    "type": "scan_complete",
-                    "status": "failed",
-                    "error": str(e),
-                })
+                progress_callback(
+                    job_id,
+                    {
+                        "type": "scan_complete",
+                        "status": "failed",
+                        "error": str(e),
+                    },
+                )
 
     def get_active_jobs(self) -> list[UploadJob]:
         """Get all currently active (non-terminal) jobs."""
diff --git a/frontend/src/hooks/useUploadJob.ts b/frontend/src/hooks/useUploadJob.ts
index f11e71c..381ba59 100644
--- a/frontend/src/hooks/useUploadJob.ts
+++ b/frontend/src/hooks/useUploadJob.ts
@@ -130,14 +130,15 @@ export function useUploadJob(options: UseUploadJobOptions = {}): UseUploadJobRes
           case "analysis_complete": {
             const evt = data as AnalysisCompleteEvent;
             setTotalFiles(evt.job.total_files);
-            // If not auto-uploading, this is terminal.
             if (!evt.auto_upload) {
+              // Analysis-only mode — this is terminal.
               setIsRunning(false);
               setJobId(null);
               setCompletedJob(evt.job);
+              setActiveFiles([]);
             }
-            // Clear active files from analysis phase.
-            setActiveFiles([]);
+            // When auto_upload is true, don't clear activeFiles — uploads
+            // may already be in progress via the pipeline.
             break;
           }
 

From 452df173518bf92c224bbcc338ec2e699121f1ba Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 13:30:24 -0700
Subject: [PATCH 126/173] Backend: Send completion messages immediately during
 upload

---
 app/services/upload_manager.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index b98eb0a..08c2ac8 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -890,6 +890,11 @@ def byte_callback(uploaded: int, total: int) -> None:
         # Clean up temp directory when upload completes
         self.cleanup_temp_dir(job_id)
 
+        # Send terminal event IMMEDIATELY so the frontend unblocks.
+        # Heavy I/O (logging, CSV, S3 sync) follows below.
+        if progress_callback:
+            progress_callback(job)
+
         uploaded_count = sum(1 for f in job.files if f.status == UploadStatus.COMPLETED)
         skipped_count = sum(1 for f in job.files if f.status == UploadStatus.SKIPPED)
         failed_count = sum(1 for f in job.files if f.status == UploadStatus.FAILED)
@@ -959,9 +964,6 @@ def byte_callback(uploaded: int, total: int) -> None:
         except Exception:
             logger.debug("Log sync to S3 failed", exc_info=True)
 
-        if progress_callback:
-            progress_callback(job)
-
     def analyze_and_upload_pipeline(
         self,
         job_id: str,
@@ -1257,6 +1259,11 @@ def byte_callback(uploaded: int, total: int) -> None:
         # Clean up temp directory
         self.cleanup_temp_dir(job_id)
 
+        # Send terminal event IMMEDIATELY so the frontend unblocks.
+        # Heavy I/O (logging, CSV, S3 sync) follows below.
+        if upload_callback:
+            upload_callback(job)
+
         uploaded_count = sum(1 for f in job.files if f.status == UploadStatus.COMPLETED)
         skipped_count = sum(1 for f in job.files if f.status == UploadStatus.SKIPPED)
         failed_count = sum(1 for f in job.files if f.status == UploadStatus.FAILED)
@@ -1325,9 +1332,6 @@ def byte_callback(uploaded: int, total: int) -> None:
         except Exception:
             logger.debug("Log sync to S3 failed", exc_info=True)
 
-        if upload_callback:
-            upload_callback(job)
-
     def cancel_job(self, job_id: str) -> bool:
         """Cancel an upload job.
 

From 925550b34ac9fad8fe43bce32d627eae16004d2d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 13:30:49 -0700
Subject: [PATCH 127/173] Frontend: Improve UI/functionality of upload page

---
 .../components/upload/UnifiedFileTable.tsx    | 103 ++++++++++++------
 1 file changed, 71 insertions(+), 32 deletions(-)

diff --git a/frontend/src/components/upload/UnifiedFileTable.tsx b/frontend/src/components/upload/UnifiedFileTable.tsx
index 9d27915..86b897e 100644
--- a/frontend/src/components/upload/UnifiedFileTable.tsx
+++ b/frontend/src/components/upload/UnifiedFileTable.tsx
@@ -1,16 +1,16 @@
 /**
  * Unified file table that persists across Review / Upload / Summary phases.
  *
- * Fixed 6-column grid — column content adapts per phase, but layout is stable.
+ * Fixed 7-column grid — column content adapts per phase, but layout is stable.
  * Uses @tanstack/react-virtual for 20K+ file handling.
  */
 
-import { memo, useCallback, useEffect, useRef } from "react";
+import { memo, useEffect, useRef, useState } from "react";
 import { useVirtualizer } from "@tanstack/react-virtual";
 
 import { formatBytes } from "../../utils/format/bytes.ts";
 import { formatDate } from "../../utils/format/date.ts";
-import { SpinnerIcon, CheckIcon, XIcon, MinusIcon, CircleIcon } from "../../utils/icons.tsx";
+import { SpinnerIcon, CheckIcon, XIcon, MinusIcon, CircleIcon, ChevronDownIcon } from "../../utils/icons.tsx";
 import type {
   SortDir,
   SortKey,
@@ -20,9 +20,17 @@ import type {
 } from "../../types/upload.ts";
 // ── Grid template (fixed across all phases) ──
 
-const GRID_COLS = "grid-cols-[36px_1fr_1fr_80px_120px_1fr]";
+const GRID_COLS = "grid-cols-[42px_36px_1fr_1fr_80px_120px_1fr]";
 const ROW_HEIGHT = 40;
 
+// Row background colors by status (uploading + summary phases only)
+const STATUS_ROW_BG: Record<string, string> = {
+  completed: "bg-green-50/70",
+  failed: "bg-red-50/70",
+  skipped: "bg-yellow-50/50",
+  in_progress: "bg-blue-50/60",
+};
+
 // ── Props ──
 
 interface UnifiedFileTableProps {
@@ -73,17 +81,31 @@ export default function UnifiedFileTable({
     prevCountRef.current = files.length;
   }, [files.length, rowVirtualizer]);
 
-  const scrollToActive = useCallback(() => {
-    const idx = files.findIndex(
-      (f) => f.status === "in_progress",
-    );
+  // ── Auto-scroll: follow the active file during upload ──
+
+  const [autoFollow, setAutoFollow] = useState(true);
+  const lastActivePathRef = useRef<string | null>(null);
+
+  // Reset auto-follow when entering upload phase
+  const prevPhaseRef = useRef(phase);
+  if (phase === "uploading" && prevPhaseRef.current !== "uploading") {
+    setAutoFollow(true);
+    lastActivePathRef.current = null;
+  }
+  prevPhaseRef.current = phase;
+
+  useEffect(() => {
+    if (phase !== "uploading" || !autoFollow) return;
+
+    const activeFile = files.find((f) => f.status === "in_progress");
+    if (!activeFile || activeFile.path === lastActivePathRef.current) return;
+
+    lastActivePathRef.current = activeFile.path;
+    const idx = files.indexOf(activeFile);
     if (idx >= 0) {
       rowVirtualizer.scrollToIndex(idx, { align: "center" });
     }
-  }, [files, rowVirtualizer]);
-
-  // Count active files for the "jump to active" button
-  const hasActiveFiles = phase === "uploading" && files.some((f) => f.status === "in_progress");
+  }, [phase, autoFollow, files, rowVirtualizer]);
 
   return (
     <div className="bg-white rounded-lg shadow-sm border border-gray-200 overflow-hidden relative">
@@ -91,7 +113,10 @@ export default function UnifiedFileTable({
       <div
         className={`grid ${GRID_COLS} gap-2 px-4 py-2 bg-gray-50 border-b border-gray-200 text-xs font-medium text-gray-500 uppercase tracking-wider`}
       >
-        {/* Col 1: Checkbox / Status icon */}
+        {/* Col 1: Row number */}
+        <div className="text-center">#</div>
+
+        {/* Col 2: Checkbox / Status icon */}
         <div className="flex items-center justify-center">
           {phase === "review" ? (
             <IndeterminateCheckbox
@@ -104,7 +129,7 @@ export default function UnifiedFileTable({
           )}
         </div>
 
-        {/* Col 2: Filename */}
+        {/* Col 3: Filename */}
         <SortHeader
           label="Filename"
           sortKey="filename"
@@ -114,7 +139,7 @@ export default function UnifiedFileTable({
           disabled={isSortFrozen}
         />
 
-        {/* Col 3: Folder */}
+        {/* Col 4: Folder */}
         <SortHeader
           label="Folder"
           sortKey="folder"
@@ -124,7 +149,7 @@ export default function UnifiedFileTable({
           disabled={isSortFrozen}
         />
 
-        {/* Col 4: Size */}
+        {/* Col 5: Size */}
         <SortHeader
           label="Size"
           sortKey="size"
@@ -135,7 +160,7 @@ export default function UnifiedFileTable({
           className="justify-end"
         />
 
-        {/* Col 5: Status */}
+        {/* Col 6: Status */}
         <SortHeader
           label="Status"
           sortKey="status"
@@ -146,7 +171,7 @@ export default function UnifiedFileTable({
           className="justify-center"
         />
 
-        {/* Col 6: Detail (context-dependent) */}
+        {/* Col 7: Detail (context-dependent) */}
         <div>
           {phase === "review" && "Modified"}
           {phase === "uploading" && ""}
@@ -178,6 +203,7 @@ export default function UnifiedFileTable({
                 <FileRow
                   key={file.path}
                   row={file}
+                  rowNumber={virtualRow.index + 1}
                   phase={phase}
                   isSelected={selectedPaths.has(file.path)}
                   onToggle={onToggleFile}
@@ -201,16 +227,20 @@ export default function UnifiedFileTable({
         {files.length.toLocaleString()} file{files.length !== 1 ? "s" : ""}
       </div>
 
-      {/* Jump to active button (upload phase only) */}
-      {hasActiveFiles && (
+      {/* Auto-scroll toggle (upload phase only) */}
+      {phase === "uploading" && (
         <button
           type="button"
-          onClick={scrollToActive}
-          className="absolute bottom-12 right-4 px-3 py-1.5 text-xs font-medium
-            bg-nlr-blue text-white rounded-full shadow-lg hover:bg-blue-700
-            transition-colors z-10"
+          onClick={() => setAutoFollow((prev) => !prev)}
+          className={`absolute bottom-12 right-4 flex items-center gap-1.5 px-3 py-1.5 text-xs font-medium
+            rounded-full shadow-lg transition-colors z-10 ${
+              autoFollow
+                ? "bg-nlr-blue text-white hover:bg-blue-700"
+                : "bg-gray-200 text-gray-600 hover:bg-gray-300"
+            }`}
         >
-          Jump to active
+          <ChevronDownIcon className="w-3.5 h-3.5" />
+          {autoFollow ? "Following active" : "Auto-scroll off"}
         </button>
       )}
     </div>
@@ -221,6 +251,7 @@ export default function UnifiedFileTable({
 
 interface FileRowProps {
   row: UnifiedFileRow;
+  rowNumber: number;
   phase: UploadPhase;
   isSelected: boolean;
   onToggle: (path: string) => void;
@@ -229,17 +260,25 @@ interface FileRowProps {
 
 const FileRow = memo(function FileRow({
   row,
+  rowNumber,
   phase,
   isSelected,
   onToggle,
   style,
 }: FileRowProps) {
+  const statusBg = phase !== "review" ? (STATUS_ROW_BG[row.status] ?? "") : "";
+
   return (
     <div
-      className={`grid ${GRID_COLS} gap-2 px-4 items-center text-xs border-b border-gray-50 hover:bg-gray-50/50`}
+      className={`grid ${GRID_COLS} gap-2 px-4 items-center text-xs border-b border-gray-50 hover:brightness-95 ${statusBg}`}
       style={style}
     >
-      {/* Col 1: Checkbox / Status icon */}
+      {/* Col 1: Row number */}
+      <span className="text-gray-400 text-center tabular-nums text-[10px]">
+        {rowNumber}
+      </span>
+
+      {/* Col 2: Checkbox / Status icon */}
       <div className="flex items-center justify-center">
         {phase === "review" ? (
           <input
@@ -253,27 +292,27 @@ const FileRow = memo(function FileRow({
         )}
       </div>
 
-      {/* Col 2: Filename */}
+      {/* Col 3: Filename */}
       <span className="text-gray-700 truncate" title={row.filename}>
         {row.filename}
       </span>
 
-      {/* Col 3: Folder */}
+      {/* Col 4: Folder */}
       <span className="text-gray-500 truncate" title={row.folder}>
         {row.folder}
       </span>
 
-      {/* Col 4: Size */}
+      {/* Col 5: Size */}
       <span className="text-gray-500 text-right tabular-nums">
         {formatBytes(row.size)}
       </span>
 
-      {/* Col 5: Status */}
+      {/* Col 6: Status */}
       <div className="flex justify-center">
         <StatusBadge status={row.status} progressPercent={row.progressPercent} phase={phase} />
       </div>
 
-      {/* Col 6: Detail */}
+      {/* Col 7: Detail */}
       <div className="text-gray-400 truncate">
         {phase === "review" && formatDate(row.mtime)}
         {phase === "uploading" && row.status === "in_progress" && (

From 37f98977befbe4ba9cbc07445c5d417b8a74cc1a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 13:46:48 -0700
Subject: [PATCH 128/173] Fix: Show individual rows as completed after they are
 done uploading

---
 app/services/upload_manager.py                  | 6 ++++++
 frontend/src/components/upload/UploadHeader.tsx | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index 08c2ac8..01689e3 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -1226,6 +1226,12 @@ def byte_callback(uploaded: int, total: int) -> None:
                                     },
                                 )
 
+                            # Notify per-file status so the frontend
+                            # updates this row immediately (the progress
+                            # dict only includes active files, so without
+                            # this the row would keep spinning).
+                            if analysis_callback:
+                                analysis_callback(job, file_state)
                             if upload_callback:
                                 upload_callback(job)
                             return None
diff --git a/frontend/src/components/upload/UploadHeader.tsx b/frontend/src/components/upload/UploadHeader.tsx
index 1c35a7d..ab9a9ef 100644
--- a/frontend/src/components/upload/UploadHeader.tsx
+++ b/frontend/src/components/upload/UploadHeader.tsx
@@ -144,9 +144,9 @@ function UploadingHeader({
       <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-4">
         <div className="flex items-center justify-between mb-2">
           <h3 className="text-sm font-semibold text-gray-900">
-            {isRunning ? "Uploading..." : "Upload Complete"}
+            {isRunning && filesProcessed < totalFiles ? "Uploading..." : "Upload Complete"}
           </h3>
-          {isRunning && <Spinner size="sm" />}
+          {isRunning && filesProcessed < totalFiles && <Spinner size="sm" />}
         </div>
 
         <ProgressBar

From 0bdea635e0ee72bb66eeb8ba41871448bc600c85 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 13:54:02 -0700
Subject: [PATCH 129/173] Linux: Add exfat4 mount permissions script

---
 setup-mount-permissions.sh | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100755 setup-mount-permissions.sh

diff --git a/setup-mount-permissions.sh b/setup-mount-permissions.sh
new file mode 100755
index 0000000..84b1c73
--- /dev/null
+++ b/setup-mount-permissions.sh
@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+# setup-mount-permissions.sh
+#
+# Configures udisks2 to mount exFAT drives with read/write permissions
+# for the current user, so the MODAQ Uploader can delete local files.
+#
+# Usage:  sudo ./setup-mount-permissions.sh [username]
+
+set -euo pipefail
+
+USER="${1:-${SUDO_USER:-}}"
+
+if [ -z "$USER" ]; then
+    echo "Error: Could not determine target user."
+    echo "Usage: sudo $0 [username]"
+    exit 1
+fi
+
+UID_NUM=$(id -u "$USER")
+GID_NUM=$(id -g "$USER")
+
+CONF="/etc/udisks2/mount_options.conf"
+
+mkdir -p /etc/udisks2
+
+cat > "$CONF" << EOF
+# MODAQ Uploader — mount exFAT drives with rw for $USER
+[defaults]
+exfat_defaults=uid=$UID_NUM,gid=$GID_NUM,dmask=0022,fmask=0133
+EOF
+
+echo "Written: $CONF"
+echo "exFAT drives will now mount with rw for $USER (uid=$UID_NUM)."
+echo ""
+echo "Unplug and re-plug the drive to apply."

From 3cf268057434251d95bf5026fd274da9577b0cfa Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:16:51 -0700
Subject: [PATCH 130/173] Linux: Point to correct modaq logo location

---
 modaq-upload.desktop.template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modaq-upload.desktop.template b/modaq-upload.desktop.template
index 6294a0d..5cf5435 100644
--- a/modaq-upload.desktop.template
+++ b/modaq-upload.desktop.template
@@ -4,7 +4,7 @@ Type=Application
 Name=MODAQ Upload
 Comment=MODAQ File Uploader
 Exec={{PROJECT_DIR}}/venv/bin/python {{PROJECT_DIR}}/launch.py
-Icon={{PROJECT_DIR}}/app/static/images/modaq-logo.png
+Icon={{PROJECT_DIR}}/frontend/public/images/modaq-logo.png
 Terminal=true
 Categories=Science;Utility;
 StartupNotify=true

From 4c2f802bac539a67725ed379cead5e88a9608976 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:19:48 -0700
Subject: [PATCH 131/173] Backend: Add delete fix permissions end point

---
 app/routes/delete.py | 74 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/app/routes/delete.py b/app/routes/delete.py
index b392c03..8c1eb2f 100644
--- a/app/routes/delete.py
+++ b/app/routes/delete.py
@@ -1,6 +1,8 @@
 """Delete API routes for local file cleanup after S3 upload."""
 
+import getpass
 import json
+import subprocess
 import threading
 import time
 from collections import deque
@@ -73,6 +75,7 @@ def scan_folder() -> tuple[Response, int]:
         return jsonify({"error": f"Permission denied: {e}"}), 403
 
     total_size = sum(f.file_size for f in job.files)
+    has_permission_issues = any(not f.writable for f in job.files)
 
     return jsonify({
         "success": True,
@@ -81,6 +84,7 @@ def scan_folder() -> tuple[Response, int]:
         "files": [f.to_dict() for f in job.files],
         "total_files": len(job.files),
         "total_size": total_size,
+        "permission_warning": has_permission_issues,
     }), 200
 
 
@@ -229,3 +233,73 @@ def cancel_delete(job_id: str) -> tuple[Response, int]:
         }), 200
 
     return jsonify({"error": "Job not found"}), 404
+
+
+@delete_bp.route("/fix-permissions", methods=["POST"])
+def fix_permissions() -> tuple[Response, int]:
+    """Fix file permissions on an ext4 external drive using sudo chown.
+
+    Runs ``sudo -S chown -R <current_user> <folder_path>`` with the
+    supplied password piped via stdin (never logged or stored).
+
+    Request body:
+        folder_path: Directory whose ownership should be fixed
+        password: The user's sudo password
+
+    Returns:
+        JSON with success status or error details
+    """
+    if not request.is_json:
+        return jsonify({"error": "JSON body required"}), 400
+
+    data = request.get_json()
+    if not data or "folder_path" not in data or "password" not in data:
+        return jsonify({"error": "folder_path and password are required"}), 400
+
+    folder_path = Path(data["folder_path"])
+    password: str = data["password"]
+
+    if not folder_path.exists():
+        return jsonify({"error": f"Folder not found: {folder_path}"}), 404
+
+    if not folder_path.is_dir():
+        return jsonify({"error": f"Path is not a directory: {folder_path}"}), 400
+
+    # Security: only allow paths under /media/ to prevent abuse
+    try:
+        resolved = folder_path.resolve()
+        if not str(resolved).startswith("/media/"):
+            return jsonify(
+                {"error": "Permission fix is only allowed for paths under /media/"}
+            ), 403
+    except (OSError, ValueError):
+        return jsonify({"error": "Invalid path"}), 400
+
+    current_user = getpass.getuser()
+
+    try:
+        result = subprocess.run(  # noqa: S603
+            ["sudo", "-S", "chown", "-R", current_user, str(resolved)],
+            input=f"{password}\n",
+            capture_output=True,
+            text=True,
+            timeout=60,
+        )
+
+        if result.returncode != 0:
+            stderr = result.stderr.strip()
+            # Strip sudo password prompt from error output
+            error_lines = [
+                line
+                for line in stderr.splitlines()
+                if not line.startswith("[sudo]") and "password" not in line.lower()
+            ]
+            error_msg = "\n".join(error_lines).strip() or "Permission fix failed"
+            return jsonify({"error": error_msg}), 500
+
+        return jsonify({"success": True}), 200
+
+    except subprocess.TimeoutExpired:
+        return jsonify({"error": "Operation timed out"}), 500
+    except Exception as e:
+        return jsonify({"error": str(e)}), 500

From 4de3600a3b5c1bc23ab094c7571b05b137439c9c Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:20:12 -0700
Subject: [PATCH 132/173] Backend: Send writeable status to the frontend

---
 app/services/delete_manager.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/app/services/delete_manager.py b/app/services/delete_manager.py
index a80fafe..f5d3b21 100644
--- a/app/services/delete_manager.py
+++ b/app/services/delete_manager.py
@@ -40,6 +40,7 @@ class FileDeleteState:
     file_size: int
     s3_path: str
     s3_bucket: str
+    writable: bool = True
     status: DeleteStatus = DeleteStatus.PENDING
     local_md5: str = ""
     s3_etag: str = ""
@@ -55,6 +56,7 @@ def to_dict(self) -> dict[str, Any]:
             "file_size": self.file_size,
             "s3_path": self.s3_path,
             "s3_bucket": self.s3_bucket,
+            "writable": self.writable,
             "status": self.status.value,
             "local_md5": self.local_md5,
             "s3_etag": self.s3_etag,
@@ -222,6 +224,7 @@ def scan_folder(
                     file_size=file_size,
                     s3_path=str(cache_info["s3_path"]),
                     s3_bucket=bucket,
+                    writable=os.access(str(mcap_path), os.W_OK),
                 )
                 job.files.append(file_state)
 

From ef9c338c34e1cf4b97895a3f53532a68d70f0b03 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:20:40 -0700
Subject: [PATCH 133/173] Frontend: Add Lock icon

---
 frontend/src/utils/icons.tsx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
index d917a5d..f52d8ae 100644
--- a/frontend/src/utils/icons.tsx
+++ b/frontend/src/utils/icons.tsx
@@ -30,6 +30,7 @@ import {
   Minus,
   Cloud,
   Circle,
+  Lock,
   type LucideProps,
 } from "lucide-react";
 
@@ -60,6 +61,7 @@ export const PlusIcon = Plus;
 export const MinusIcon = Minus;
 export const CloudIcon = Cloud;
 export const CircleIcon = Circle;
+export const LockIcon = Lock;
 
 // Export type for icon props
 export type { LucideProps as IconProps };

From 1b4bb36cc007d3c7d4bd7fa3958fc2cacf8676e2 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:21:01 -0700
Subject: [PATCH 134/173] Frontend: Add Fix permissions flow for delete

---
 .../components/delete/FixPermissionsModal.tsx | 148 ++++++++++++++++++
 frontend/src/hooks/useDeleteScan.ts           |   2 +-
 frontend/src/pages/DeletePage.tsx             |  48 +++++-
 frontend/src/stores/deleteStore.ts            |  14 +-
 frontend/src/types/delete.ts                  |   2 +
 5 files changed, 208 insertions(+), 6 deletions(-)
 create mode 100644 frontend/src/components/delete/FixPermissionsModal.tsx

diff --git a/frontend/src/components/delete/FixPermissionsModal.tsx b/frontend/src/components/delete/FixPermissionsModal.tsx
new file mode 100644
index 0000000..f1437ba
--- /dev/null
+++ b/frontend/src/components/delete/FixPermissionsModal.tsx
@@ -0,0 +1,148 @@
+import { useCallback, useState } from "react";
+
+import { apiPost } from "../../api/client.ts";
+import { LockIcon, SpinnerIcon, SuccessIcon, WarningIcon } from "../../utils/icons.tsx";
+import Modal from "../common/Modal.tsx";
+
+interface FixPermissionsModalProps {
+  isOpen: boolean;
+  onClose: () => void;
+  folderPath: string;
+  onFixed: () => void;
+}
+
+export default function FixPermissionsModal({
+  isOpen,
+  onClose,
+  folderPath,
+  onFixed,
+}: FixPermissionsModalProps) {
+  const [password, setPassword] = useState("");
+  const [isLoading, setIsLoading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [success, setSuccess] = useState(false);
+
+  const handleSubmit = useCallback(
+    async (e: React.FormEvent) => {
+      e.preventDefault();
+      if (!password.trim()) return;
+
+      setIsLoading(true);
+      setError(null);
+
+      try {
+        await apiPost("/api/delete/fix-permissions", {
+          folder_path: folderPath,
+          password,
+        });
+        setSuccess(true);
+        setPassword("");
+        onFixed();
+      } catch (err) {
+        const msg =
+          err instanceof Error ? err.message : "Failed to fix permissions";
+        setError(msg);
+      } finally {
+        setIsLoading(false);
+      }
+    },
+    [password, folderPath, onFixed],
+  );
+
+  const handleClose = useCallback(() => {
+    setPassword("");
+    setError(null);
+    setSuccess(false);
+    onClose();
+  }, [onClose]);
+
+  return (
+    <Modal
+      isOpen={isOpen}
+      onClose={handleClose}
+      title="Fix Permissions"
+      footer={
+        !success ? (
+          <div className="flex gap-3">
+            <button
+              type="button"
+              onClick={handleClose}
+              className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
+            >
+              Cancel
+            </button>
+            <button
+              type="submit"
+              form="fix-permissions-form"
+              disabled={isLoading || !password.trim()}
+              className="px-4 py-2 text-sm font-medium rounded transition-colors bg-nlr-blue text-white hover:bg-nlr-blue-light disabled:bg-gray-300 disabled:cursor-not-allowed flex items-center gap-2"
+            >
+              {isLoading && (
+                <SpinnerIcon className="w-4 h-4 animate-spin" />
+              )}
+              Fix Permissions
+            </button>
+          </div>
+        ) : (
+          <button
+            type="button"
+            onClick={handleClose}
+            className="px-4 py-2 text-sm font-medium rounded transition-colors bg-nlr-blue text-white hover:bg-nlr-blue-light"
+          >
+            Close
+          </button>
+        )
+      }
+    >
+      {success ? (
+        <div className="flex items-start gap-3 p-3 bg-green-50 rounded-lg border border-green-200">
+          <SuccessIcon className="w-5 h-5 text-green-600 flex-shrink-0 mt-0.5" />
+          <p className="text-sm text-green-800">
+            Permissions fixed successfully. The scan results will be refreshed.
+          </p>
+        </div>
+      ) : (
+        <form id="fix-permissions-form" onSubmit={handleSubmit} className="space-y-4">
+          <div className="flex items-start gap-3 p-3 bg-amber-50 rounded-lg border border-amber-200">
+            <LockIcon className="w-5 h-5 text-amber-600 flex-shrink-0 mt-0.5" />
+            <div className="text-sm text-amber-800">
+              <p>
+                The files on this drive are owned by a different user. Your sudo
+                password is needed to change ownership so files can be deleted.
+              </p>
+              <p className="mt-1 text-amber-700">
+                Your password is sent directly to the system and is never stored
+                or logged.
+              </p>
+            </div>
+          </div>
+
+          <div>
+            <label
+              htmlFor="sudo-password"
+              className="block text-sm font-medium text-gray-700 mb-1"
+            >
+              Sudo Password
+            </label>
+            <input
+              id="sudo-password"
+              type="password"
+              value={password}
+              onChange={(e) => setPassword(e.target.value)}
+              placeholder="Enter your password"
+              autoFocus
+              className="w-full px-3 py-2 border border-gray-300 rounded-md text-sm focus:outline-none focus:ring-2 focus:ring-nlr-blue focus:border-transparent"
+            />
+          </div>
+
+          {error && (
+            <div className="flex items-start gap-2 p-3 bg-red-50 rounded-lg border border-red-200">
+              <WarningIcon className="w-4 h-4 text-red-600 flex-shrink-0 mt-0.5" />
+              <p className="text-sm text-red-700">{error}</p>
+            </div>
+          )}
+        </form>
+      )}
+    </Modal>
+  );
+}
diff --git a/frontend/src/hooks/useDeleteScan.ts b/frontend/src/hooks/useDeleteScan.ts
index 1bde0c9..c9e8435 100644
--- a/frontend/src/hooks/useDeleteScan.ts
+++ b/frontend/src/hooks/useDeleteScan.ts
@@ -36,7 +36,7 @@ export function useDeleteScan(): UseDeleteScanResult {
         }
         const res = await apiPost<DeleteScanResponse>("/api/delete/scan", body);
         setDeleteJobId(res.job_id);
-        setScanResults(res.files, res.total_size);
+        setScanResults(res.files, res.total_size, res.permission_warning);
       } finally {
         setIsScanning(false);
       }
diff --git a/frontend/src/pages/DeletePage.tsx b/frontend/src/pages/DeletePage.tsx
index 782dbf1..992074f 100644
--- a/frontend/src/pages/DeletePage.tsx
+++ b/frontend/src/pages/DeletePage.tsx
@@ -8,13 +8,14 @@
  * Step 5: Summary with results
  */
 
-import { useCallback, useEffect, useMemo, useState } from "react";
+import { useCallback, useEffect, useMemo, useRef, useState } from "react";
 
 import ProgressBar from "../components/common/ProgressBar.tsx";
 import Spinner from "../components/common/Spinner.tsx";
 import StatCard from "../components/common/StatCard.tsx";
 import DeleteConfirmation from "../components/delete/DeleteConfirmation.tsx";
 import DeleteStepper from "../components/delete/DeleteStepper.tsx";
+import FixPermissionsModal from "../components/delete/FixPermissionsModal.tsx";
 import CancelConfirmModal from "../components/upload/CancelConfirmModal.tsx";
 import FolderBrowser from "../components/upload/FolderBrowser.tsx";
 import type { FolderExclusions } from "../components/upload/FolderBrowser.tsx";
@@ -23,6 +24,7 @@ import { useDeleteScan } from "../hooks/useDeleteScan.ts";
 import { useAppStore } from "../stores/appStore.ts";
 import { useDeleteStore, type DeleteStep } from "../stores/deleteStore.ts";
 import type { DeleteScanFile } from "../types/delete.ts";
+import { LockIcon, WarningIcon } from "../utils/icons.tsx";
 import { formatBytes } from "../utils/format/bytes.ts";
 
 /** Status badge colors for file table. */
@@ -61,6 +63,7 @@ export default function DeletePage() {
     setFolderPath,
     scanResults,
     scanTotalSize,
+    permissionWarning,
     completedJob,
     isDeleting,
     reset,
@@ -77,12 +80,17 @@ export default function DeletePage() {
   const [page, setPage] = useState(0);
   const pageSize = 50;
   const [showCancelModal, setShowCancelModal] = useState(false);
+  const [showFixPermModal, setShowFixPermModal] = useState(false);
   const [refreshKey, setRefreshKey] = useState(0);
 
+  // Track exclusions so re-scan after permission fix uses the same filters
+  const lastExclusions = useRef<FolderExclusions | undefined>(undefined);
+
   // ── Step transitions ──
 
   const handleFolderSelected = useCallback(
     async (path: string, exclusions?: FolderExclusions) => {
+      lastExclusions.current = exclusions;
       setFolderPath(path);
       setStep(2);
       await scan(path, exclusions);
@@ -90,6 +98,12 @@ export default function DeletePage() {
     [setFolderPath, setStep, scan],
   );
 
+  const handlePermissionsFixed = useCallback(async () => {
+    if (folderPath) {
+      await scan(folderPath, lastExclusions.current);
+    }
+  }, [folderPath, scan]);
+
   const handleConfirmDelete = useCallback(async () => {
     setStep(4);
     await deleteJob.startDelete();
@@ -196,6 +210,29 @@ export default function DeletePage() {
             />
           </div>
 
+          {permissionWarning && (
+            <div className="bg-amber-50 border border-amber-200 rounded-lg p-4 flex items-start gap-3">
+              <LockIcon className="w-5 h-5 text-amber-600 flex-shrink-0 mt-0.5" />
+              <div className="flex-1">
+                <p className="text-sm font-medium text-amber-800">
+                  Permission issues detected
+                </p>
+                <p className="text-sm text-amber-700 mt-1">
+                  Some files on this drive are owned by a different user and
+                  cannot be deleted without fixing permissions first.
+                </p>
+                <button
+                  type="button"
+                  onClick={() => setShowFixPermModal(true)}
+                  className="mt-2 inline-flex items-center gap-1.5 px-3 py-1.5 text-sm font-medium text-amber-800 bg-amber-100 border border-amber-300 rounded-md hover:bg-amber-200"
+                >
+                  <WarningIcon className="w-4 h-4" />
+                  Fix Permissions
+                </button>
+              </div>
+            </div>
+          )}
+
           {scanResults.length === 0 && !isScanning && (
             <div className="bg-amber-50 border border-amber-200 rounded-lg p-4 text-sm text-amber-800">
               No uploaded MCAP files found in this folder. Only files previously
@@ -286,13 +323,20 @@ export default function DeletePage() {
               <button
                 type="button"
                 onClick={() => setStep(3)}
-                disabled={isScanning}
+                disabled={isScanning || permissionWarning}
                 className="px-4 py-2 text-sm font-medium text-white bg-red-600 rounded-md hover:bg-red-700 disabled:bg-gray-300 disabled:cursor-not-allowed"
               >
                 Continue to Confirmation
               </button>
             )}
           </div>
+
+          <FixPermissionsModal
+            isOpen={showFixPermModal}
+            onClose={() => setShowFixPermModal(false)}
+            folderPath={folderPath}
+            onFixed={handlePermissionsFixed}
+          />
         </div>
       )}
 
diff --git a/frontend/src/stores/deleteStore.ts b/frontend/src/stores/deleteStore.ts
index 44c1bfa..09ddcb9 100644
--- a/frontend/src/stores/deleteStore.ts
+++ b/frontend/src/stores/deleteStore.ts
@@ -15,8 +15,14 @@ interface DeleteState {
   // Scan results
   scanResults: DeleteScanFile[];
   scanTotalSize: number;
+  permissionWarning: boolean;
   isScanning: boolean;
-  setScanResults: (files: DeleteScanFile[], totalSize: number) => void;
+  setScanResults: (
+    files: DeleteScanFile[],
+    totalSize: number,
+    permissionWarning: boolean,
+  ) => void;
+  setPermissionWarning: (warning: boolean) => void;
   setIsScanning: (scanning: boolean) => void;
 
   // Delete job
@@ -36,6 +42,7 @@ const initialState = {
   folderPath: "",
   scanResults: [] as DeleteScanFile[],
   scanTotalSize: 0,
+  permissionWarning: false,
   isScanning: false,
   deleteJobId: null,
   completedJob: null,
@@ -48,8 +55,9 @@ export const useDeleteStore = create<DeleteState>((set) => ({
   setStep: (step) => set({ step }),
   setFolderPath: (folderPath) => set({ folderPath }),
 
-  setScanResults: (scanResults, scanTotalSize) =>
-    set({ scanResults, scanTotalSize }),
+  setScanResults: (scanResults, scanTotalSize, permissionWarning) =>
+    set({ scanResults, scanTotalSize, permissionWarning }),
+  setPermissionWarning: (permissionWarning) => set({ permissionWarning }),
   setIsScanning: (isScanning) => set({ isScanning }),
 
   setDeleteJobId: (deleteJobId) => set({ deleteJobId }),
diff --git a/frontend/src/types/delete.ts b/frontend/src/types/delete.ts
index 0547bcf..7f1e21d 100644
--- a/frontend/src/types/delete.ts
+++ b/frontend/src/types/delete.ts
@@ -21,6 +21,7 @@ export interface DeleteScanFile {
   file_size: number;
   s3_path: string;
   s3_bucket: string;
+  writable: boolean;
   status: DeleteFileStatus;
   local_md5: string;
   s3_etag: string;
@@ -36,6 +37,7 @@ export interface DeleteScanResponse {
   files: DeleteScanFile[];
   total_files: number;
   total_size: number;
+  permission_warning: boolean;
 }
 
 // ── SSE event types ──

From 3359dc7d41172fece718219d488a08cc960aa45b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:41:05 -0700
Subject: [PATCH 135/173] Fix: Actually stop upload when user requests
 cancellation

---
 app/routes/files.py            |  8 +++++
 app/services/s3_service.py     | 23 +++++++++++--
 app/services/upload_manager.py | 61 +++++++++++++++++++++++++++++-----
 3 files changed, 82 insertions(+), 10 deletions(-)

diff --git a/app/routes/files.py b/app/routes/files.py
index 067e784..fddc02d 100644
--- a/app/routes/files.py
+++ b/app/routes/files.py
@@ -241,6 +241,11 @@ def _walk_error(err: OSError) -> None:
         {"name": "Home", "path": str(Path.home())},
     ]
 
+    # Add SURFWEC SSD as the top priority quick link
+    surfwec_ssd = Path("/media/m2/SURFWEC_SSD")
+    if surfwec_ssd.exists() and surfwec_ssd.is_dir():
+        quick_links.append({"name": "SURFWEC_SSD", "path": str(surfwec_ssd)})
+
     # Add Volumes on macOS
     volumes_path = Path("/Volumes")
     if volumes_path.exists():
@@ -279,6 +284,9 @@ def _walk_error(err: OSError) -> None:
                     children = []
                 if children:
                     for child in sorted(children, key=lambda x: x.name.lower()):
+                        # Already added SURFWEC_SSD above
+                        if child == surfwec_ssd:
+                            continue
                         quick_links.append({"name": child.name, "path": str(child)})
                 else:
                     quick_links.append({"name": entry.name, "path": entry_str})
diff --git a/app/services/s3_service.py b/app/services/s3_service.py
index 5b80a27..362e3a1 100644
--- a/app/services/s3_service.py
+++ b/app/services/s3_service.py
@@ -10,6 +10,10 @@
 from botocore.exceptions import ClientError, NoCredentialsError
 from mypy_boto3_s3 import S3Client
 
+
+class UploadCancelledError(Exception):
+    """Raised when an upload is cancelled mid-transfer."""
+
 # Multipart threshold: files below this size are uploaded as a single PUT request,
 # which produces a simple MD5 ETag. Files above use multipart upload, which produces
 # a composite ETag (md5_of_part_md5s-part_count) that can't be compared to a local MD5.
@@ -101,6 +105,7 @@ def upload_file_with_progress(
     bucket: str,
     key: str,
     callback: Callable[[int, int], None] | None = None,
+    cancel_check: Callable[[], bool] | None = None,
 ) -> dict[str, Any]:
     """Upload a file to S3 with progress tracking.
 
@@ -110,9 +115,15 @@ def upload_file_with_progress(
         bucket: S3 bucket name
         key: S3 object key
         callback: Progress callback function (bytes_uploaded, total_bytes)
+        cancel_check: Callable that returns True if the upload should be cancelled.
+            Checked on every progress callback (each chunk). When True, raises
+            UploadCancelledError to abort the boto3 transfer immediately.
 
     Returns:
         Dictionary with upload result information
+
+    Raises:
+        UploadCancelledError: If cancel_check returns True during upload
     """
     file_path = Path(path)
     file_size = file_path.stat().st_size
@@ -121,18 +132,24 @@ class ProgressCallback:
         """Callback class for tracking upload progress."""
 
         def __init__(
-            self, total_size: int, user_callback: Callable[[int, int], None] | None
+            self,
+            total_size: int,
+            user_callback: Callable[[int, int], None] | None,
+            should_cancel: Callable[[], bool] | None,
         ) -> None:
             self.total_size = total_size
             self.uploaded = 0
             self.user_callback = user_callback
+            self.should_cancel = should_cancel
 
         def __call__(self, bytes_amount: int) -> None:
+            if self.should_cancel and self.should_cancel():
+                raise UploadCancelledError(f"Upload cancelled for {key}")
             self.uploaded += bytes_amount
             if self.user_callback:
                 self.user_callback(self.uploaded, self.total_size)
 
-    progress = ProgressCallback(file_size, callback)
+    progress = ProgressCallback(file_size, callback, cancel_check)
 
     try:
         client.upload_file(
@@ -150,6 +167,8 @@ def __call__(self, bytes_amount: int) -> None:
             "size": file_size,
             "error": None,
         }
+    except UploadCancelledError:
+        raise
     except ClientError as e:
         return {
             "success": False,
diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index 01689e3..b8e7fd9 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -16,6 +16,7 @@
 from app.services import mcap_service, s3_service
 from app.services.cache_service import get_cache_service
 from app.services.log_service import get_log_service
+from app.services.s3_service import UploadCancelledError
 from app.services.utils import format_file_size
 
 logger = logging.getLogger(__name__)
@@ -608,6 +609,11 @@ def analyze_job_async(
                 for file_state in job.files
             }
             for future in as_completed(parse_futures):
+                if job.cancelled:
+                    for pending_future in parse_futures:
+                        pending_future.cancel()
+                    break
+
                 file_state = parse_futures[future]
                 result = future.result()
                 if isinstance(result, str):
@@ -776,6 +782,11 @@ def make_upload_task(
                     fs: FileUploadState,
                 ) -> Callable[[], Any]:
                     def upload_task() -> Any:
+                        if job.cancelled:
+                            with job.lock:
+                                fs.status = UploadStatus.CANCELLED
+                            return None
+
                         # Mark UPLOADING inside the worker so files stay READY until picked up
                         with job.lock:
                             fs.status = UploadStatus.UPLOADING
@@ -806,6 +817,7 @@ def byte_callback(uploaded: int, total: int) -> None:
                             s3_bucket,
                             fs.s3_path,
                             byte_callback,
+                            cancel_check=lambda: job.cancelled,
                         )
 
                     return upload_task
@@ -815,12 +827,12 @@ def byte_callback(uploaded: int, total: int) -> None:
 
             # Process results as they complete
             for future in as_completed(futures):
-                if job.cancelled:
-                    break
-
                 file_state = futures[future]
                 try:
                     result = future.result()
+                    if result is None:
+                        # Task was cancelled before starting
+                        continue
                     file_state.upload_completed_at = datetime.now(UTC)
                     if result["success"]:
                         file_state.status = UploadStatus.COMPLETED
@@ -862,6 +874,10 @@ def byte_callback(uploaded: int, total: int) -> None:
                                 "error": file_state.error_message,
                             },
                         )
+                except UploadCancelledError:
+                    with job.lock:
+                        file_state.status = UploadStatus.CANCELLED
+                        file_state.upload_completed_at = datetime.now(UTC)
                 except Exception as e:
                     file_state.upload_completed_at = datetime.now(UTC)
                     file_state.status = UploadStatus.FAILED
@@ -1038,6 +1054,9 @@ def analyze_and_upload_pipeline(
 
                 for future in as_completed(parse_futures):
                     if job.cancelled:
+                        # Cancel remaining parse futures that haven't started yet
+                        for pending_future in parse_futures:
+                            pending_future.cancel()
                         break
 
                     fs = parse_futures[future]
@@ -1128,6 +1147,10 @@ def upload_task() -> Any:
                             if job.cancelled:
                                 with job.lock:
                                     file_state.status = UploadStatus.CANCELLED
+                                if analysis_callback:
+                                    analysis_callback(job, file_state)
+                                if upload_callback:
+                                    upload_callback(job)
                                 return None
 
                             try:
@@ -1160,6 +1183,7 @@ def byte_callback(uploaded: int, total: int) -> None:
                                     s3_bucket,
                                     file_state.s3_path,
                                     byte_callback,
+                                    cancel_check=lambda: job.cancelled,
                                 )
 
                                 # Handle completion inline
@@ -1211,6 +1235,10 @@ def byte_callback(uploaded: int, total: int) -> None:
                                             "error": file_state.error_message,
                                         },
                                     )
+                            except UploadCancelledError:
+                                with job.lock:
+                                    file_state.status = UploadStatus.CANCELLED
+                                    file_state.upload_completed_at = datetime.now(UTC)
                             except Exception as e:
                                 file_state.upload_completed_at = datetime.now(UTC)
                                 file_state.status = UploadStatus.FAILED
@@ -1248,8 +1276,20 @@ def byte_callback(uploaded: int, total: int) -> None:
                 {"job_id": job_id, "error": str(e)},
             )
         finally:
-            # Wait for all in-flight uploads to complete
-            upload_executor.shutdown(wait=True)
+            # Wait for in-flight uploads; cancel_work_items prevents queued tasks from starting
+            upload_executor.shutdown(wait=True, cancel_futures=True)
+
+            # Mark any files still in non-terminal states as cancelled
+            if job.cancelled:
+                with job.lock:
+                    for fs in job.files:
+                        if fs.status in (
+                            UploadStatus.PENDING,
+                            UploadStatus.READY,
+                            UploadStatus.ANALYZING,
+                            UploadStatus.UPLOADING,
+                        ):
+                            fs.status = UploadStatus.CANCELLED
 
         # Final job status
         job.completed_at = datetime.now(UTC)
@@ -1352,9 +1392,14 @@ def cancel_job(self, job_id: str) -> bool:
             return False
 
         job.cancelled = True
-        for file_state in job.files:
-            if file_state.status in (UploadStatus.PENDING, UploadStatus.READY):
-                file_state.status = UploadStatus.CANCELLED
+        with job.lock:
+            for file_state in job.files:
+                if file_state.status in (
+                    UploadStatus.PENDING,
+                    UploadStatus.READY,
+                    UploadStatus.ANALYZING,
+                ):
+                    file_state.status = UploadStatus.CANCELLED
 
         # Clean up temp directory when job is cancelled
         self.cleanup_temp_dir(job_id)

From b85851b3fb125c1d2422a97574b08083eefd71f0 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:47:18 -0700
Subject: [PATCH 136/173] Feature: Add graceful shutdown button

---
 app/routes/settings.py                        | 28 +++++++++++++
 .../src/components/settings/DangerZone.tsx    | 39 +++++++++++++++++++
 frontend/src/utils/icons.tsx                  |  2 +
 3 files changed, 69 insertions(+)

diff --git a/app/routes/settings.py b/app/routes/settings.py
index 486f72c..2f46c47 100644
--- a/app/routes/settings.py
+++ b/app/routes/settings.py
@@ -1,5 +1,9 @@
 """Settings API routes for modaq_upload"""
 
+import os
+import signal
+import threading
+
 from flask import Blueprint, Response, jsonify, request
 
 from app.config import get_package_version, get_settings, get_updater
@@ -247,6 +251,30 @@ def invalidate_cache() -> tuple[Response, int]:
     ), 200
 
 
+@settings_bp.route("/shutdown", methods=["POST"])
+def shutdown_server() -> tuple[Response, int]:
+    """Gracefully shut down the application server.
+
+    Sends SIGINT to the current process after a brief delay so the
+    HTTP response can be returned to the client first.
+
+    Returns:
+        JSON response confirming shutdown was initiated
+    """
+    log = get_log_service()
+    log.info("app", "shutdown_requested", "Graceful shutdown requested via settings UI")
+
+    def _shutdown() -> None:
+        os.kill(os.getpid(), signal.SIGINT)
+
+    # Delay slightly so the response reaches the client
+    timer = threading.Timer(0.5, _shutdown)
+    timer.daemon = True
+    timer.start()
+
+    return jsonify({"success": True, "message": "Server is shutting down..."}), 200
+
+
 @settings_bp.route("/cache/sync", methods=["POST"])
 def sync_cache_with_s3() -> tuple[Response, int]:
     """Sync cache with S3, marking deleted files as non-existent.
diff --git a/frontend/src/components/settings/DangerZone.tsx b/frontend/src/components/settings/DangerZone.tsx
index 8a5ba39..9f61bbd 100644
--- a/frontend/src/components/settings/DangerZone.tsx
+++ b/frontend/src/components/settings/DangerZone.tsx
@@ -1,6 +1,7 @@
 import { useState } from "react";
 import { apiPost } from "../../api/client.ts";
 import { useAppStore } from "../../stores/appStore.ts";
+import { PowerIcon } from "../../utils/icons.tsx";
 
 const DEFAULT_SETTINGS = {
   aws_profile: "default",
@@ -16,6 +17,7 @@ export default function DangerZone() {
 
   const [clearing, setClearing] = useState(false);
   const [resetting, setResetting] = useState(false);
+  const [shuttingDown, setShuttingDown] = useState(false);
 
   async function handleClearCache() {
     if (!window.confirm("Are you sure you want to clear the upload cache? This cannot be undone.")) {
@@ -59,6 +61,25 @@ export default function DangerZone() {
     }
   }
 
+  async function handleShutdown() {
+    if (
+      !window.confirm(
+        "Are you sure you want to shut down the server? You will need to restart it manually.",
+      )
+    ) {
+      return;
+    }
+
+    setShuttingDown(true);
+    try {
+      await apiPost<{ success: boolean; message: string }>("/api/settings/shutdown");
+      addNotification("info", "Server is shutting down...");
+    } catch {
+      addNotification("error", "Failed to shut down server");
+      setShuttingDown(false);
+    }
+  }
+
   return (
     <div className="bg-white rounded-lg shadow p-6 border-2 border-red-300">
       <h3 className="text-lg font-semibold text-red-600 mb-2">Danger Zone</h3>
@@ -100,6 +121,24 @@ export default function DangerZone() {
             {resetting ? "Resetting..." : "Reset Settings"}
           </button>
         </div>
+
+        <div className="flex items-center justify-between p-3 rounded-md border border-red-200 bg-red-50/50">
+          <div>
+            <div className="text-sm font-medium text-nlr-text">Shutdown Server</div>
+            <div className="text-xs text-gray-500">
+              Gracefully shuts down the application. You will need to restart it manually.
+            </div>
+          </div>
+          <button
+            type="button"
+            onClick={handleShutdown}
+            disabled={shuttingDown}
+            className="ml-4 px-4 py-2 text-sm font-medium text-red-600 border border-red-300 rounded-md hover:bg-red-600 hover:text-white disabled:opacity-50 disabled:cursor-not-allowed transition-colors whitespace-nowrap inline-flex items-center gap-1.5"
+          >
+            <PowerIcon className="h-4 w-4" />
+            {shuttingDown ? "Shutting down..." : "Shutdown"}
+          </button>
+        </div>
       </div>
     </div>
   );
diff --git a/frontend/src/utils/icons.tsx b/frontend/src/utils/icons.tsx
index f52d8ae..4a5a2c2 100644
--- a/frontend/src/utils/icons.tsx
+++ b/frontend/src/utils/icons.tsx
@@ -31,6 +31,7 @@ import {
   Cloud,
   Circle,
   Lock,
+  Power,
   type LucideProps,
 } from "lucide-react";
 
@@ -62,6 +63,7 @@ export const MinusIcon = Minus;
 export const CloudIcon = Cloud;
 export const CircleIcon = Circle;
 export const LockIcon = Lock;
+export const PowerIcon = Power;
 
 // Export type for icon props
 export type { LucideProps as IconProps };

From 42d5faa1fd11b42e7b9cb85019aa4a9319e79b15 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Wed, 18 Feb 2026 14:51:53 -0700
Subject: [PATCH 137/173] Fix: Make graceful shutdown work when ran via
 gunicorn

---
 app/routes/settings.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/app/routes/settings.py b/app/routes/settings.py
index 2f46c47..7f2d2d0 100644
--- a/app/routes/settings.py
+++ b/app/routes/settings.py
@@ -2,6 +2,7 @@
 
 import os
 import signal
+import sys
 import threading
 
 from flask import Blueprint, Response, jsonify, request
@@ -255,8 +256,13 @@ def invalidate_cache() -> tuple[Response, int]:
 def shutdown_server() -> tuple[Response, int]:
     """Gracefully shut down the application server.
 
-    Sends SIGINT to the current process after a brief delay so the
-    HTTP response can be returned to the client first.
+    Detects whether we're running under gunicorn or the Flask dev server
+    and sends the appropriate signal after a brief delay so the HTTP
+    response can be returned to the client first.
+
+    - Gunicorn: sends SIGTERM to the master (parent) process, which
+      triggers a graceful shutdown of all workers.
+    - Flask dev server: sends SIGINT to the current process.
 
     Returns:
         JSON response confirming shutdown was initiated
@@ -265,7 +271,12 @@ def shutdown_server() -> tuple[Response, int]:
     log.info("app", "shutdown_requested", "Graceful shutdown requested via settings UI")
 
     def _shutdown() -> None:
-        os.kill(os.getpid(), signal.SIGINT)
+        if "gunicorn" in sys.modules:
+            # Under gunicorn, the worker's parent is the master process.
+            # SIGTERM tells the master to finish active requests and exit.
+            os.kill(os.getppid(), signal.SIGTERM)
+        else:
+            os.kill(os.getpid(), signal.SIGINT)
 
     # Delay slightly so the response reaches the client
     timer = threading.Timer(0.5, _shutdown)

From 45bdd016e14ce0853908b72090d7311f5bec9845 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 06:59:12 -0700
Subject: [PATCH 138/173] Backend: Refactor to use batch processing

---
 app/services/batch_processor.py | 433 ++++++++++++++++++++++++++++++
 app/services/job_storage.py     | 455 ++++++++++++++++++++++++++++++++
 2 files changed, 888 insertions(+)
 create mode 100644 app/services/batch_processor.py
 create mode 100644 app/services/job_storage.py

diff --git a/app/services/batch_processor.py b/app/services/batch_processor.py
new file mode 100644
index 0000000..a2c161e
--- /dev/null
+++ b/app/services/batch_processor.py
@@ -0,0 +1,433 @@
+"""Batch processing infrastructure for handling large upload/delete operations."""
+
+import logging
+import os
+import time
+from collections.abc import Callable
+from dataclasses import dataclass
+from datetime import UTC, datetime
+from enum import Enum
+from typing import Any
+
+import psutil
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class BatchConfig:
+    """Configuration for batch processing behavior."""
+
+    enabled: bool = True
+    batch_size: int = 100
+    auto_tune_workers: bool = True
+    max_workers: int = 4
+    target_cpu_percent: float = 70.0
+    skip_mcap_validation: bool = False
+    use_database_for_large_jobs: bool = True
+    large_job_threshold: int = 1000
+
+    @classmethod
+    def from_dict(cls, data: dict[str, Any]) -> "BatchConfig":
+        """Create BatchConfig from dictionary."""
+        return cls(
+            enabled=data.get("enabled", True),
+            batch_size=data.get("batch_size", 100),
+            auto_tune_workers=data.get("auto_tune_workers", True),
+            max_workers=data.get("max_workers", 4),
+            target_cpu_percent=data.get("target_cpu_percent", 70.0),
+            skip_mcap_validation=data.get("skip_mcap_validation", False),
+            use_database_for_large_jobs=data.get("use_database_for_large_jobs", True),
+            large_job_threshold=data.get("large_job_threshold", 1000),
+        )
+
+
+class BatchStatus(Enum):
+    """Status of a batch within a job."""
+
+    PENDING = "pending"
+    PROCESSING = "processing"
+    COMPLETED = "completed"
+    FAILED = "failed"
+    CANCELLED = "cancelled"
+
+
+@dataclass
+class BatchState:
+    """State tracking for an individual batch within a job."""
+
+    batch_id: int
+    total_batches: int
+    files_in_batch: int
+    status: BatchStatus = BatchStatus.PENDING
+    files_processed: int = 0
+    files_uploaded: int = 0
+    files_failed: int = 0
+    bytes_uploaded: int = 0
+    started_at: datetime | None = None
+    completed_at: datetime | None = None
+    error_message: str = ""
+
+    @property
+    def duration_seconds(self) -> float | None:
+        """Calculate batch processing duration in seconds."""
+        if self.started_at and self.completed_at:
+            return (self.completed_at - self.started_at).total_seconds()
+        return None
+
+    def to_dict(self) -> dict[str, Any]:
+        """Convert to dictionary for JSON serialization."""
+        return {
+            "batch_id": self.batch_id,
+            "total_batches": self.total_batches,
+            "files_in_batch": self.files_in_batch,
+            "status": self.status.value,
+            "files_processed": self.files_processed,
+            "files_uploaded": self.files_uploaded,
+            "files_failed": self.files_failed,
+            "bytes_uploaded": self.bytes_uploaded,
+            "started_at": self.started_at.isoformat() if self.started_at else None,
+            "completed_at": self.completed_at.isoformat() if self.completed_at else None,
+            "duration_seconds": self.duration_seconds,
+            "error_message": self.error_message,
+        }
+
+
+class WorkerAutoTuner:
+    """Monitors system resources and adjusts worker count dynamically."""
+
+    def __init__(
+        self,
+        target_cpu_percent: float = 70.0,
+        check_interval_seconds: float = 30.0,
+        max_workers: int = 16,
+    ) -> None:
+        """Initialize the auto-tuner.
+
+        Args:
+            target_cpu_percent: Target CPU utilization (0-100)
+            check_interval_seconds: Time between adjustment checks
+            max_workers: Maximum allowed workers (hard ceiling)
+        """
+        self.target_cpu_percent = target_cpu_percent
+        self.check_interval_seconds = check_interval_seconds
+        self.max_workers = max_workers
+        self.cpu_count = os.cpu_count() or 4
+        self.last_check_time = 0.0
+        self.history: list[dict[str, Any]] = []
+
+    def should_check(self) -> bool:
+        """Check if enough time has passed for another adjustment."""
+        now = time.time()
+        return (now - self.last_check_time) >= self.check_interval_seconds
+
+    def adjust_if_needed(self, current_workers: int) -> int:
+        """Adjust worker count based on current system utilization.
+
+        Args:
+            current_workers: Current number of workers
+
+        Returns:
+            Recommended worker count (may be same as current)
+        """
+        if not self.should_check():
+            return current_workers
+
+        self.last_check_time = time.time()
+
+        # Measure CPU and memory
+        try:
+            cpu_percent = psutil.cpu_percent(interval=1.0)
+            memory_info = psutil.virtual_memory()
+            memory_percent = memory_info.percent
+
+            # Record metrics
+            self.history.append(
+                {
+                    "timestamp": time.time(),
+                    "cpu_percent": cpu_percent,
+                    "memory_percent": memory_percent,
+                    "workers": current_workers,
+                }
+            )
+
+            # Keep only last 10 measurements
+            if len(self.history) > 10:
+                self.history = self.history[-10:]
+
+            logger.info(
+                f"Auto-tuner: CPU={cpu_percent:.1f}%, Memory={memory_percent:.1f}%, "
+                f"Workers={current_workers}"
+            )
+
+            # Start conservative on first check
+            if len(self.history) == 1:
+                recommended = min(4, self.cpu_count - 1, self.max_workers)
+                logger.info(f"Auto-tuner: Initial worker count: {recommended}")
+                return max(2, recommended)
+
+            # Decrease if overloaded
+            if cpu_percent > self.target_cpu_percent + 10 or memory_percent > 85:
+                new_workers = max(2, current_workers - 1)
+                logger.info(
+                    f"Auto-tuner: Decreasing workers {current_workers} → {new_workers} "
+                    f"(CPU overload or low memory)"
+                )
+                return new_workers
+
+            # Increase if underutilized
+            if cpu_percent < self.target_cpu_percent - 10:
+                new_workers = min(
+                    current_workers + 2,
+                    self.cpu_count,
+                    self.max_workers,
+                )
+                if new_workers > current_workers:
+                    logger.info(
+                        f"Auto-tuner: Increasing workers {current_workers} → {new_workers} "
+                        f"(CPU underutilized)"
+                    )
+                return new_workers
+
+            # No change needed
+            return current_workers
+
+        except Exception as e:
+            logger.warning(f"Auto-tuner: Error checking system resources: {e}")
+            return current_workers
+
+    def get_metrics(self) -> dict[str, Any]:
+        """Get current tuning metrics."""
+        if not self.history:
+            return {
+                "cpu_percent": None,
+                "memory_percent": None,
+                "workers": None,
+                "history_size": 0,
+            }
+
+        latest = self.history[-1]
+        return {
+            "cpu_percent": latest["cpu_percent"],
+            "memory_percent": latest["memory_percent"],
+            "workers": latest["workers"],
+            "history_size": len(self.history),
+            "target_cpu_percent": self.target_cpu_percent,
+        }
+
+
+def split_into_batches(items: list[Any], batch_size: int) -> list[list[Any]]:
+    """Split a list of items into batches of specified size.
+
+    Args:
+        items: List of items to split
+        batch_size: Maximum items per batch
+
+    Returns:
+        List of batches (each batch is a list of items)
+
+    Example:
+        >>> split_into_batches([1, 2, 3, 4, 5], 2)
+        [[1, 2], [3, 4], [5]]
+    """
+    if batch_size <= 0:
+        raise ValueError("batch_size must be positive")
+
+    batches = []
+    for i in range(0, len(items), batch_size):
+        batches.append(items[i : i + batch_size])
+
+    return batches
+
+
+class BatchProcessor:
+    """Orchestrates batch-by-batch processing for large jobs."""
+
+    def __init__(self, config: BatchConfig) -> None:
+        """Initialize batch processor.
+
+        Args:
+            config: Batch processing configuration
+        """
+        self.config = config
+        self.tuner: WorkerAutoTuner | None = None
+
+        if config.auto_tune_workers:
+            self.tuner = WorkerAutoTuner(
+                target_cpu_percent=config.target_cpu_percent,
+                check_interval_seconds=30.0,
+                max_workers=min(config.max_workers, 16),
+            )
+
+    def should_use_batch_processing(self, total_files: int) -> bool:
+        """Determine if batch processing should be used for this job.
+
+        Args:
+            total_files: Total number of files in job
+
+        Returns:
+            True if batch processing should be used
+        """
+        if not self.config.enabled:
+            return False
+
+        # Use batch processing for jobs exceeding threshold
+        return total_files >= self.config.large_job_threshold
+
+    def create_batches(self, items: list[Any], batch_size: int | None = None) -> list[list[Any]]:
+        """Create batches from a list of items.
+
+        Args:
+            items: Items to batch
+            batch_size: Override default batch size (optional)
+
+        Returns:
+            List of batches
+        """
+        size = batch_size if batch_size is not None else self.config.batch_size
+        return split_into_batches(items, size)
+
+    def process_batches(
+        self,
+        items: list[Any],
+        process_fn: Callable[[list[Any], int, int], dict[str, Any]],
+        progress_callback: Callable[[BatchState], None] | None = None,
+        check_cancelled: Callable[[], bool] | None = None,
+    ) -> dict[str, Any]:
+        """Process items in batches with progress tracking.
+
+        Args:
+            items: Items to process
+            process_fn: Function to process each batch, receives:
+                - batch items
+                - batch_id (0-indexed)
+                - total_batches
+                Returns dict with 'success', 'processed', 'failed', 'bytes_uploaded'
+            progress_callback: Optional callback for batch progress updates
+            check_cancelled: Optional function to check if job was cancelled
+
+        Returns:
+            Summary dict with total stats: {
+                'success': bool,
+                'total_processed': int,
+                'total_uploaded': int,
+                'total_failed': int,
+                'total_bytes': int,
+                'batches_completed': int,
+                'batches_failed': int,
+                'duration_seconds': float
+            }
+        """
+        batches = self.create_batches(items)
+        total_batches = len(batches)
+
+        logger.info(
+            f"Batch processor: Processing {len(items)} items in {total_batches} batches "
+            f"(batch_size={self.config.batch_size})"
+        )
+
+        # Tracking stats
+        total_processed = 0
+        total_uploaded = 0
+        total_failed = 0
+        total_bytes = 0
+        batches_completed = 0
+        batches_failed = 0
+
+        start_time = time.time()
+
+        for batch_id, batch_items in enumerate(batches):
+            # Check for cancellation
+            if check_cancelled and check_cancelled():
+                logger.info("Batch processor: Job cancelled by user")
+                break
+
+            # Create batch state
+            batch_state = BatchState(
+                batch_id=batch_id,
+                total_batches=total_batches,
+                files_in_batch=len(batch_items),
+                status=BatchStatus.PROCESSING,
+                started_at=datetime.now(UTC),
+            )
+
+            # Notify progress callback
+            if progress_callback:
+                progress_callback(batch_state)
+
+            try:
+                # Process this batch
+                result = process_fn(batch_items, batch_id, total_batches)
+
+                # Update batch state with results
+                batch_state.files_processed = result.get("processed", 0)
+                batch_state.files_uploaded = result.get("uploaded", 0)
+                batch_state.files_failed = result.get("failed", 0)
+                batch_state.bytes_uploaded = result.get("bytes_uploaded", 0)
+                batch_state.status = (
+                    BatchStatus.COMPLETED if result.get("success") else BatchStatus.FAILED
+                )
+                batch_state.completed_at = datetime.now(UTC)
+
+                # Update totals
+                total_processed += batch_state.files_processed
+                total_uploaded += batch_state.files_uploaded
+                total_failed += batch_state.files_failed
+                total_bytes += batch_state.bytes_uploaded
+
+                if batch_state.status == BatchStatus.COMPLETED:
+                    batches_completed += 1
+                else:
+                    batches_failed += 1
+
+                logger.info(
+                    f"Batch {batch_id + 1}/{total_batches} completed: "
+                    f"{batch_state.files_uploaded} uploaded, {batch_state.files_failed} failed"
+                )
+
+            except Exception as e:
+                logger.error(f"Batch {batch_id + 1}/{total_batches} failed: {e}", exc_info=True)
+                batch_state.status = BatchStatus.FAILED
+                batch_state.error_message = str(e)
+                batch_state.completed_at = datetime.now(UTC)
+                batches_failed += 1
+
+            # Notify progress callback with final state
+            if progress_callback:
+                progress_callback(batch_state)
+
+            # Auto-tune workers between batches
+            if self.tuner:
+                # This would be used by the caller to adjust ThreadPoolExecutor
+                new_workers = self.tuner.adjust_if_needed(self.config.max_workers)
+                if new_workers != self.config.max_workers:
+                    logger.info(f"Auto-tuner recommends {new_workers} workers")
+
+        # Calculate final stats
+        duration = time.time() - start_time
+
+        summary = {
+            "success": batches_failed == 0,
+            "total_processed": total_processed,
+            "total_uploaded": total_uploaded,
+            "total_failed": total_failed,
+            "total_bytes": total_bytes,
+            "batches_completed": batches_completed,
+            "batches_failed": batches_failed,
+            "total_batches": total_batches,
+            "duration_seconds": duration,
+        }
+
+        logger.info(
+            f"Batch processing complete: {batches_completed}/{total_batches} batches succeeded, "
+            f"{total_uploaded} items uploaded, {total_failed} failed, "
+            f"{duration:.1f}s elapsed"
+        )
+
+        return summary
+
+    def get_tuner_metrics(self) -> dict[str, Any]:
+        """Get current auto-tuner metrics."""
+        if self.tuner:
+            return self.tuner.get_metrics()
+        return {"enabled": False}
diff --git a/app/services/job_storage.py b/app/services/job_storage.py
new file mode 100644
index 0000000..4d3b7b3
--- /dev/null
+++ b/app/services/job_storage.py
@@ -0,0 +1,455 @@
+"""Database-backed storage for large upload/delete jobs."""
+
+import json
+import logging
+import sqlite3
+import threading
+from datetime import UTC, datetime, timedelta
+from typing import Any
+
+from app.config import BASE_DIR
+
+logger = logging.getLogger(__name__)
+
+# Database file location
+DB_FILE = BASE_DIR / "upload_jobs.db"
+
+# SQL schema
+SCHEMA_SQL = """
+CREATE TABLE IF NOT EXISTS upload_jobs (
+    job_id TEXT PRIMARY KEY,
+    job_type TEXT NOT NULL,
+    status TEXT NOT NULL,
+    total_files INTEGER NOT NULL,
+    files_processed INTEGER DEFAULT 0,
+    files_uploaded INTEGER DEFAULT 0,
+    files_failed INTEGER DEFAULT 0,
+    total_bytes INTEGER DEFAULT 0,
+    created_at TEXT NOT NULL,
+    started_at TEXT,
+    completed_at TEXT,
+    metadata TEXT
+);
+
+CREATE TABLE IF NOT EXISTS upload_files (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    job_id TEXT NOT NULL,
+    filename TEXT NOT NULL,
+    local_path TEXT NOT NULL,
+    file_size INTEGER NOT NULL,
+    status TEXT NOT NULL,
+    s3_path TEXT,
+    start_time TEXT,
+    bytes_uploaded INTEGER DEFAULT 0,
+    error_message TEXT,
+    is_duplicate INTEGER DEFAULT 0,
+    is_valid INTEGER DEFAULT 1,
+    upload_started_at TEXT,
+    upload_completed_at TEXT,
+    FOREIGN KEY (job_id) REFERENCES upload_jobs(job_id)
+);
+
+CREATE INDEX IF NOT EXISTS idx_upload_files_job_id ON upload_files(job_id);
+CREATE INDEX IF NOT EXISTS idx_upload_files_status ON upload_files(status);
+CREATE INDEX IF NOT EXISTS idx_upload_jobs_created_at ON upload_jobs(created_at);
+"""
+
+
+class JobStorage:
+    """SQLite-backed storage for upload/delete jobs."""
+
+    _instance: "JobStorage | None" = None
+    _lock = threading.Lock()
+
+    def __new__(cls) -> "JobStorage":
+        """Singleton pattern to ensure only one storage instance."""
+        if cls._instance is None:
+            with cls._lock:
+                if cls._instance is None:
+                    cls._instance = super().__new__(cls)
+                    cls._instance._initialize_db()
+        return cls._instance
+
+    def _initialize_db(self) -> None:
+        """Initialize the database and create tables if needed."""
+        try:
+            conn = sqlite3.connect(str(DB_FILE), check_same_thread=False)
+            conn.executescript(SCHEMA_SQL)
+            conn.commit()
+            conn.close()
+            logger.info(f"Job storage database initialized at {DB_FILE}")
+        except Exception as e:
+            logger.error(f"Failed to initialize job storage database: {e}", exc_info=True)
+            raise
+
+    def _get_connection(self) -> sqlite3.Connection:
+        """Get a database connection."""
+        conn = sqlite3.connect(str(DB_FILE), check_same_thread=False)
+        conn.row_factory = sqlite3.Row
+        return conn
+
+    def save_job(
+        self,
+        job_id: str,
+        job_type: str,
+        total_files: int,
+        file_states: list[dict[str, Any]],
+        metadata: dict[str, Any] | None = None,
+    ) -> None:
+        """Save a new job to the database.
+
+        Args:
+            job_id: Unique job identifier
+            job_type: Type of job ('upload' or 'delete')
+            total_files: Total number of files in job
+            file_states: List of file state dictionaries
+            metadata: Optional job metadata
+        """
+        try:
+            conn = self._get_connection()
+            cursor = conn.cursor()
+
+            # Insert job record
+            cursor.execute(
+                """
+                INSERT INTO upload_jobs (
+                    job_id, job_type, status, total_files, created_at, metadata
+                )
+                VALUES (?, ?, ?, ?, ?, ?)
+                """,
+                (
+                    job_id,
+                    job_type,
+                    "pending",
+                    total_files,
+                    datetime.now(UTC).isoformat(),
+                    json.dumps(metadata) if metadata else None,
+                ),
+            )
+
+            # Insert file records
+            for file_state in file_states:
+                cursor.execute(
+                    """
+                    INSERT INTO upload_files (
+                        job_id, filename, local_path, file_size, status,
+                        s3_path, start_time, is_duplicate, is_valid
+                    )
+                    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+                    """,
+                    (
+                        job_id,
+                        file_state.get("filename", ""),
+                        file_state.get("local_path", ""),
+                        file_state.get("file_size", 0),
+                        file_state.get("status", "pending"),
+                        file_state.get("s3_path", ""),
+                        file_state.get("start_time"),
+                        1 if file_state.get("is_duplicate", False) else 0,
+                        1 if file_state.get("is_valid", True) else 0,
+                    ),
+                )
+
+            conn.commit()
+            conn.close()
+            logger.info(f"Saved job {job_id} with {len(file_states)} files to database")
+
+        except Exception as e:
+            logger.error(f"Failed to save job {job_id}: {e}", exc_info=True)
+            raise
+
+    def update_job_status(
+        self,
+        job_id: str,
+        status: str,
+        files_processed: int | None = None,
+        files_uploaded: int | None = None,
+        files_failed: int | None = None,
+        total_bytes: int | None = None,
+        started_at: datetime | None = None,
+        completed_at: datetime | None = None,
+    ) -> None:
+        """Update job status and statistics.
+
+        Args:
+            job_id: Job identifier
+            status: New job status
+            files_processed: Number of files processed (optional)
+            files_uploaded: Number of files uploaded (optional)
+            files_failed: Number of files failed (optional)
+            total_bytes: Total bytes uploaded (optional)
+            started_at: Job start time (optional)
+            completed_at: Job completion time (optional)
+        """
+        try:
+            conn = self._get_connection()
+            cursor = conn.cursor()
+
+            # Build dynamic UPDATE query
+            updates = ["status = ?"]
+            params: list[Any] = [status]
+
+            if files_processed is not None:
+                updates.append("files_processed = ?")
+                params.append(files_processed)
+
+            if files_uploaded is not None:
+                updates.append("files_uploaded = ?")
+                params.append(files_uploaded)
+
+            if files_failed is not None:
+                updates.append("files_failed = ?")
+                params.append(files_failed)
+
+            if total_bytes is not None:
+                updates.append("total_bytes = ?")
+                params.append(total_bytes)
+
+            if started_at is not None:
+                updates.append("started_at = ?")
+                params.append(started_at.isoformat())
+
+            if completed_at is not None:
+                updates.append("completed_at = ?")
+                params.append(completed_at.isoformat())
+
+            params.append(job_id)
+
+            query = f"UPDATE upload_jobs SET {', '.join(updates)} WHERE job_id = ?"
+            cursor.execute(query, params)
+
+            conn.commit()
+            conn.close()
+
+        except Exception as e:
+            logger.error(f"Failed to update job {job_id}: {e}", exc_info=True)
+            raise
+
+    def update_file_status(
+        self,
+        job_id: str,
+        filename: str,
+        status: str,
+        bytes_uploaded: int | None = None,
+        error_message: str | None = None,
+        upload_started_at: datetime | None = None,
+        upload_completed_at: datetime | None = None,
+    ) -> None:
+        """Update status of a specific file in a job.
+
+        Args:
+            job_id: Job identifier
+            filename: Filename to update
+            status: New file status
+            bytes_uploaded: Bytes uploaded (optional)
+            error_message: Error message (optional)
+            upload_started_at: Upload start time (optional)
+            upload_completed_at: Upload completion time (optional)
+        """
+        try:
+            conn = self._get_connection()
+            cursor = conn.cursor()
+
+            # Build dynamic UPDATE query
+            updates = ["status = ?"]
+            params: list[Any] = [status]
+
+            if bytes_uploaded is not None:
+                updates.append("bytes_uploaded = ?")
+                params.append(bytes_uploaded)
+
+            if error_message is not None:
+                updates.append("error_message = ?")
+                params.append(error_message)
+
+            if upload_started_at is not None:
+                updates.append("upload_started_at = ?")
+                params.append(upload_started_at.isoformat())
+
+            if upload_completed_at is not None:
+                updates.append("upload_completed_at = ?")
+                params.append(upload_completed_at.isoformat())
+
+            params.extend([job_id, filename])
+
+            query = (
+                f"UPDATE upload_files SET {', '.join(updates)} WHERE job_id = ? AND filename = ?"
+            )
+            cursor.execute(query, params)
+
+            conn.commit()
+            conn.close()
+
+        except Exception as e:
+            logger.error(f"Failed to update file {filename} in job {job_id}: {e}", exc_info=True)
+
+    def get_job(self, job_id: str) -> dict[str, Any] | None:
+        """Get job metadata by ID.
+
+        Args:
+            job_id: Job identifier
+
+        Returns:
+            Job metadata dict or None if not found
+        """
+        try:
+            conn = self._get_connection()
+            cursor = conn.cursor()
+
+            cursor.execute(
+                """
+                SELECT job_id, job_type, status, total_files,
+                       files_processed, files_uploaded, files_failed, total_bytes,
+                       created_at, started_at, completed_at, metadata
+                FROM upload_jobs
+                WHERE job_id = ?
+                """,
+                (job_id,),
+            )
+
+            row = cursor.fetchone()
+            conn.close()
+
+            if row is None:
+                return None
+
+            return {
+                "job_id": row["job_id"],
+                "job_type": row["job_type"],
+                "status": row["status"],
+                "total_files": row["total_files"],
+                "files_processed": row["files_processed"],
+                "files_uploaded": row["files_uploaded"],
+                "files_failed": row["files_failed"],
+                "total_bytes": row["total_bytes"],
+                "created_at": row["created_at"],
+                "started_at": row["started_at"],
+                "completed_at": row["completed_at"],
+                "metadata": json.loads(row["metadata"]) if row["metadata"] else {},
+            }
+
+        except Exception as e:
+            logger.error(f"Failed to get job {job_id}: {e}", exc_info=True)
+            return None
+
+    def get_job_results(self, job_id: str, page: int = 1, per_page: int = 100) -> dict[str, Any]:
+        """Get paginated file results for a job.
+
+        Args:
+            job_id: Job identifier
+            page: Page number (1-indexed)
+            per_page: Results per page (default 100)
+
+        Returns:
+            Dict with 'files' list and pagination info
+        """
+        try:
+            conn = self._get_connection()
+            cursor = conn.cursor()
+
+            # Get total count
+            cursor.execute("SELECT COUNT(*) as count FROM upload_files WHERE job_id = ?", (job_id,))
+            total_files = cursor.fetchone()["count"]
+
+            # Get paginated files
+            offset = (page - 1) * per_page
+            cursor.execute(
+                """
+                SELECT filename, local_path, file_size, status, s3_path,
+                       start_time, bytes_uploaded, error_message,
+                       is_duplicate, is_valid, upload_started_at, upload_completed_at
+                FROM upload_files
+                WHERE job_id = ?
+                ORDER BY id
+                LIMIT ? OFFSET ?
+                """,
+                (job_id, per_page, offset),
+            )
+
+            files = []
+            for row in cursor.fetchall():
+                files.append(
+                    {
+                        "filename": row["filename"],
+                        "local_path": row["local_path"],
+                        "file_size": row["file_size"],
+                        "status": row["status"],
+                        "s3_path": row["s3_path"],
+                        "start_time": row["start_time"],
+                        "bytes_uploaded": row["bytes_uploaded"],
+                        "error_message": row["error_message"],
+                        "is_duplicate": bool(row["is_duplicate"]),
+                        "is_valid": bool(row["is_valid"]),
+                        "upload_started_at": row["upload_started_at"],
+                        "upload_completed_at": row["upload_completed_at"],
+                    }
+                )
+
+            conn.close()
+
+            total_pages = (total_files + per_page - 1) // per_page
+
+            return {
+                "job_id": job_id,
+                "files": files,
+                "pagination": {
+                    "page": page,
+                    "per_page": per_page,
+                    "total_files": total_files,
+                    "total_pages": total_pages,
+                    "has_next": page < total_pages,
+                    "has_prev": page > 1,
+                },
+            }
+
+        except Exception as e:
+            logger.error(f"Failed to get results for job {job_id}: {e}", exc_info=True)
+            return {"job_id": job_id, "files": [], "pagination": {}}
+
+    def cleanup_old_jobs(self, days: int = 7) -> int:
+        """Delete jobs older than specified days.
+
+        Args:
+            days: Age threshold in days
+
+        Returns:
+            Number of jobs deleted
+        """
+        try:
+            cutoff_date = datetime.now(UTC) - timedelta(days=days)
+            conn = self._get_connection()
+            cursor = conn.cursor()
+
+            # Delete old files first (foreign key constraint)
+            cursor.execute(
+                """
+                DELETE FROM upload_files
+                WHERE job_id IN (
+                    SELECT job_id FROM upload_jobs
+                    WHERE created_at < ?
+                )
+                """,
+                (cutoff_date.isoformat(),),
+            )
+
+            # Delete old jobs
+            cursor.execute(
+                "DELETE FROM upload_jobs WHERE created_at < ?",
+                (cutoff_date.isoformat(),),
+            )
+
+            deleted_count = cursor.rowcount
+            conn.commit()
+            conn.close()
+
+            logger.info(f"Cleaned up {deleted_count} jobs older than {days} days")
+            return deleted_count
+
+        except Exception as e:
+            logger.error(f"Failed to cleanup old jobs: {e}", exc_info=True)
+            return 0
+
+
+def get_job_storage() -> JobStorage:
+    """Get the singleton JobStorage instance."""
+    return JobStorage()

From fc545ee43ce56cc4472290a7b9f96c69cf101639 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:03:13 -0700
Subject: [PATCH 139/173] Dev: Add psutil requirement

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 8f31002..3db7f7f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,3 +5,4 @@ python-dotenv>=1.0.0
 gunicorn>=21.0.0
 modaq_toolkit[mcap] @ git+https://github.com/MODAQ2/MODAQ_toolkit.git
 mcap-ros2-support
+psutil>=5.9.0

From fe3b802041b3e416c482a9f81597bfb8d2c290c9 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:04:06 -0700
Subject: [PATCH 140/173] Config: Add batch processing spec

---
 app/config.py | 58 ++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 10 deletions(-)

diff --git a/app/config.py b/app/config.py
index 4f78506..e79d22e 100644
--- a/app/config.py
+++ b/app/config.py
@@ -58,6 +58,7 @@ class Settings:
 
     _instance: "Settings | None" = None
     _settings: dict[str, Any]
+    _provenance: dict[str, dict[str, str]]
 
     def __new__(cls) -> "Settings":
         """Singleton pattern to ensure only one settings instance exists."""
@@ -83,34 +84,58 @@ def _load_settings(self) -> None:
             "default_upload_folder": "",
             "display_name": "MODAQ Uploader",
             "log_directory": "logs",
+            "batch_processing": {
+                "enabled": True,
+                "batch_size": 100,
+                "auto_tune_workers": True,
+                "max_workers": 4,
+                "target_cpu_percent": 70.0,
+                "skip_mcap_validation": False,
+                "use_database_for_large_jobs": True,
+                "large_job_threshold": 1000,
+            },
         }
 
+        # Track the source of each setting value as it is applied layer by layer.
+        provenance: dict[str, dict[str, str]] = {k: {"source": "builtin"} for k in defaults}
+
         # Load from settings.default.json if it exists
         if SETTINGS_DEFAULT_FILE.exists():
             with open(SETTINGS_DEFAULT_FILE, encoding="utf-8") as f:
-                defaults.update(json.load(f))
+                default_data = json.load(f)
+            defaults.update(default_data)
+            for k in default_data:
+                provenance[k] = {"source": "default_file", "path": str(SETTINGS_DEFAULT_FILE)}
 
         # Load from settings.json if it exists
         if SETTINGS_FILE.exists():
             with open(SETTINGS_FILE, encoding="utf-8") as f:
-                defaults.update(json.load(f))
+                user_data = json.load(f)
+            defaults.update(user_data)
+            for k in user_data:
+                provenance[k] = {"source": "settings_file", "path": str(SETTINGS_FILE)}
 
         # Override with environment variables (highest priority)
-        env_overrides = {
-            "aws_profile": os.environ.get(ENV_AWS_PROFILE),
-            "aws_region": os.environ.get(ENV_AWS_REGION),
-            "s3_bucket": os.environ.get(ENV_S3_BUCKET),
-            "default_upload_folder": os.environ.get(ENV_DEFAULT_UPLOAD_FOLDER),
-            "display_name": os.environ.get(ENV_DISPLAY_NAME),
-            "log_directory": os.environ.get(ENV_LOG_DIRECTORY),
+        env_overrides: dict[str, tuple[str | None, str]] = {
+            "aws_profile": (os.environ.get(ENV_AWS_PROFILE), ENV_AWS_PROFILE),
+            "aws_region": (os.environ.get(ENV_AWS_REGION), ENV_AWS_REGION),
+            "s3_bucket": (os.environ.get(ENV_S3_BUCKET), ENV_S3_BUCKET),
+            "default_upload_folder": (
+                os.environ.get(ENV_DEFAULT_UPLOAD_FOLDER),
+                ENV_DEFAULT_UPLOAD_FOLDER,
+            ),
+            "display_name": (os.environ.get(ENV_DISPLAY_NAME), ENV_DISPLAY_NAME),
+            "log_directory": (os.environ.get(ENV_LOG_DIRECTORY), ENV_LOG_DIRECTORY),
         }
 
         # Only apply non-None environment values
-        for key, value in env_overrides.items():
+        for key, (value, env_var) in env_overrides.items():
             if value is not None:
                 defaults[key] = value
+                provenance[key] = {"source": "env", "env_var": env_var}
 
         self._settings = defaults
+        self._provenance = provenance
 
         # Save settings.json if it doesn't exist
         if not SETTINGS_FILE.exists():
@@ -139,6 +164,10 @@ def all(self) -> dict[str, Any]:
         """Get all settings as a dictionary."""
         return self._settings.copy()
 
+    def to_response(self) -> dict[str, Any]:
+        """Return settings with value_sources provenance for API responses."""
+        return {**self._settings, "value_sources": self._provenance}
+
     def reload(self) -> None:
         """Reload settings from file."""
         self._load_settings()
@@ -177,6 +206,15 @@ def log_directory(self) -> Path:
             path = BASE_DIR / path
         return path
 
+    @property
+    def batch_processing(self) -> dict[str, Any]:
+        """Get batch processing configuration."""
+        return dict(self._settings.get("batch_processing", {}))
+
+    def get_batch_config(self) -> dict[str, Any]:
+        """Get batch processing configuration (alias for batch_processing property)."""
+        return self.batch_processing
+
 
 def get_settings() -> Settings:
     """Get the singleton Settings instance."""

From e4c45b6d5c3c71190904b473555b771f8d51bcd8 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:04:38 -0700
Subject: [PATCH 141/173] Backend: Handle delete in 1k file batches

---
 app/routes/delete.py | 103 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 83 insertions(+), 20 deletions(-)

diff --git a/app/routes/delete.py b/app/routes/delete.py
index 8c1eb2f..7f4b518 100644
--- a/app/routes/delete.py
+++ b/app/routes/delete.py
@@ -77,15 +77,17 @@ def scan_folder() -> tuple[Response, int]:
     total_size = sum(f.file_size for f in job.files)
     has_permission_issues = any(not f.writable for f in job.files)
 
-    return jsonify({
-        "success": True,
-        "job_id": job.job_id,
-        "folder_path": str(folder_path.absolute()),
-        "files": [f.to_dict() for f in job.files],
-        "total_files": len(job.files),
-        "total_size": total_size,
-        "permission_warning": has_permission_issues,
-    }), 200
+    return jsonify(
+        {
+            "success": True,
+            "job_id": job.job_id,
+            "folder_path": str(folder_path.absolute()),
+            "files": [f.to_dict() for f in job.files],
+            "total_files": len(job.files),
+            "total_size": total_size,
+            "permission_warning": has_permission_issues,
+        }
+    ), 200
 
 
 @delete_bp.route("/start/<job_id>", methods=["POST"])
@@ -110,9 +112,11 @@ def progress_callback(job: DeleteJob) -> None:
         if job.status in ("completed", "failed", "cancelled"):
             _send_sse_event(job.job_id, {"type": "delete_complete", **job.to_dict()})
         else:
-            _send_sse_event(
-                job.job_id, {"type": "delete_progress", **job.to_progress_dict()}
-            )
+            _send_sse_event(job.job_id, {"type": "delete_progress", **job.to_progress_dict()})
+
+    def batch_callback(batch_event: dict[str, Any]) -> None:
+        """Send batch-level events via SSE."""
+        _send_sse_event(job_id, batch_event)
 
     def run_delete() -> None:
         manager.start_delete_job(
@@ -120,6 +124,7 @@ def run_delete() -> None:
             settings.aws_profile,
             settings.aws_region,
             progress_callback=progress_callback,
+            batch_callback=batch_callback,
         )
 
     thread = threading.Thread(target=run_delete, daemon=True)
@@ -212,6 +217,64 @@ def get_status(job_id: str) -> tuple[Response, int]:
     return jsonify(job.to_dict()), 200
 
 
+@delete_bp.route("/results/<job_id>", methods=["GET"])
+def get_results(job_id: str) -> tuple[Response, int]:
+    """Get paginated results for a completed delete job.
+
+    For large jobs (>1000 files), results can be retrieved in pages
+    to prevent memory overload and large response payloads.
+
+    Args:
+        job_id: The delete job to get results for
+
+    Query parameters:
+        page: Page number (default: 1)
+        per_page: Results per page (default: 100, max: 500)
+
+    Returns:
+        JSON response with paginated file results and job metadata
+    """
+    manager = get_delete_manager()
+
+    # Get the job
+    job = manager.get_job(job_id)
+    if not job:
+        return jsonify({"error": "Job not found"}), 404
+
+    # Parse pagination parameters
+    page = request.args.get("page", 1, type=int)
+    per_page = min(request.args.get("per_page", 100, type=int), 500)
+
+    # Calculate pagination
+    total_files = len(job.files)
+    total_pages = (total_files + per_page - 1) // per_page
+    offset = (page - 1) * per_page
+    paginated_files = job.files[offset : offset + per_page]
+
+    # Build response
+    return jsonify(
+        {
+            "job_id": job_id,
+            "files": [f.to_dict() for f in paginated_files],
+            "pagination": {
+                "page": page,
+                "per_page": per_page,
+                "total_files": total_files,
+                "total_pages": total_pages,
+                "has_next": page < total_pages,
+                "has_prev": page > 1,
+            },
+            "job_metadata": {
+                "job_id": job.job_id,
+                "status": job.status,
+                "total_files": total_files,
+                "status_counts": job.to_progress_dict().get("status_counts", {}),
+                "total_deleted_size": job.to_progress_dict().get("total_deleted_size", 0),
+            },
+        }
+    ), 200
+
+
 @delete_bp.route("/cancel/<job_id>", methods=["POST"])
 def cancel_delete(job_id: str) -> tuple[Response, int]:
     """Cancel a delete job.
@@ -226,11 +289,13 @@ def cancel_delete(job_id: str) -> tuple[Response, int]:
 
     if manager.cancel_job(job_id):
         job = manager.get_job(job_id)
-        return jsonify({
-            "success": True,
-            "job_id": job_id,
-            "job": job.to_dict() if job else None,
-        }), 200
+        return jsonify(
+            {
+                "success": True,
+                "job_id": job_id,
+                "job": job.to_dict() if job else None,
+            }
+        ), 200
 
     return jsonify({"error": "Job not found"}), 404
 
@@ -269,9 +334,7 @@ def fix_permissions() -> tuple[Response, int]:
     try:
         resolved = folder_path.resolve()
         if not str(resolved).startswith("/media/"):
-            return jsonify(
-                {"error": "Permission fix is only allowed for paths under /media/"}
-            ), 403
+            return jsonify({"error": "Permission fix is only allowed for paths under /media/"}), 403
     except (OSError, ValueError):
         return jsonify({"error": "Invalid path"}), 400
 

From cc23c6ade6b56c2db921043f97dda54550b3cdbe Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:05:17 -0700
Subject: [PATCH 142/173] Dev: Lint

---
 app/routes/files.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/app/routes/files.py b/app/routes/files.py
index fddc02d..3237814 100644
--- a/app/routes/files.py
+++ b/app/routes/files.py
@@ -175,9 +175,9 @@ def _walk_error(err: OSError) -> None:
             except OSError:
                 continue
 
-            uploaded = cache.check_exists_by_filename(
-                bucket, mcap_path.name, file_stat.st_size
-            ) is True
+            uploaded = (
+                cache.check_exists_by_filename(bucket, mcap_path.name, file_stat.st_size) is True
+            )
 
             if len(parts) == 1:
                 # Direct child MCAP file
@@ -276,9 +276,7 @@ def _walk_error(err: OSError) -> None:
                 # If it's a user directory (e.g. /media/username), list its children
                 try:
                     children = [
-                        c
-                        for c in entry.iterdir()
-                        if c.is_dir() and not c.name.startswith(".")
+                        c for c in entry.iterdir() if c.is_dir() and not c.name.startswith(".")
                     ]
                 except PermissionError:
                     children = []

From 7b4d930164ef9136e7d79244cdcc6114b20924e4 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:06:08 -0700
Subject: [PATCH 143/173] Backend: Do a smart merge of settings from different
 locations

---
 app/routes/settings.py | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/app/routes/settings.py b/app/routes/settings.py
index 7f2d2d0..f58fb9a 100644
--- a/app/routes/settings.py
+++ b/app/routes/settings.py
@@ -4,6 +4,7 @@
 import signal
 import sys
 import threading
+from typing import Any
 
 from flask import Blueprint, Response, jsonify, request
 
@@ -23,7 +24,7 @@ def get_all_settings() -> tuple[Response, int]:
         JSON response with all settings
     """
     settings = get_settings()
-    return jsonify(settings.all()), 200
+    return jsonify(settings.to_response()), 200
 
 
 @settings_bp.route("", methods=["PUT"])
@@ -45,12 +46,17 @@ def update_settings() -> tuple[Response, int]:
 
     settings = get_settings()
 
-    # Validate settings
-    allowed_keys = {
-        "aws_profile", "aws_region", "s3_bucket", "default_upload_folder", "display_name",
-        "log_directory",
-    }
-    filtered_data = {k: v for k, v in data.items() if k in allowed_keys}
+    # Accept any key present in the current settings schema; deep-merge nested dicts
+    # (e.g. batch_processing) so callers can send partial sub-objects.
+    current = settings.all()
+    filtered_data: dict[str, Any] = {}
+    for k, v in data.items():
+        if k not in current:
+            continue
+        if isinstance(current[k], dict) and isinstance(v, dict):
+            filtered_data[k] = {**current[k], **v}
+        else:
+            filtered_data[k] = v
 
     if not filtered_data:
         return jsonify({"error": "No valid settings provided"}), 400
@@ -65,7 +71,7 @@ def update_settings() -> tuple[Response, int]:
         {"changed_keys": list(filtered_data.keys())},
     )
 
-    return jsonify(settings.all()), 200
+    return jsonify(settings.to_response()), 200
 
 
 @settings_bp.route("/profiles", methods=["GET"])

From 094945ebe20662f86c5a936abb3011c03b17413e Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:07:04 -0700
Subject: [PATCH 144/173] Backend: Refactor upload to be more efficient

---
 app/routes/upload.py | 183 ++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 173 insertions(+), 10 deletions(-)

diff --git a/app/routes/upload.py b/app/routes/upload.py
index e93daa4..cd4cb74 100644
--- a/app/routes/upload.py
+++ b/app/routes/upload.py
@@ -23,16 +23,55 @@
 
 # Store for SSE clients per job
 _sse_queues: dict[str, list[deque[dict[str, Any]]]] = {}
+_sse_events: dict[str, threading.Event] = {}  # Events to signal new data (replaces polling)
+_sse_timestamps: dict[str, float] = {}  # Track last activity for TTL cleanup
 _sse_lock = threading.Lock()
 
+# Configuration
+SSE_QUEUE_TTL_SECONDS = 3600  # Clean up queues after 1 hour of inactivity
+SSE_HEARTBEAT_INTERVAL_SECONDS = 15  # Send heartbeat every 15 seconds
+
+
+def _cleanup_old_sse_queues() -> int:
+    """Clean up SSE queues that haven't been accessed recently.
+
+    Returns:
+        Number of queues removed
+    """
+    now = time.time()
+    removed = 0
+    with _sse_lock:
+        expired = [
+            job_id
+            for job_id, timestamp in _sse_timestamps.items()
+            if now - timestamp > SSE_QUEUE_TTL_SECONDS
+        ]
+        for job_id in expired:
+            _sse_queues.pop(job_id, None)
+            _sse_events.pop(job_id, None)
+            _sse_timestamps.pop(job_id, None)
+            removed += 1
+    return removed
+
 
 def send_sse_event(job_id: str, data: dict[str, Any]) -> None:
-    """Send an SSE event to all clients listening for a job."""
+    """Send an SSE event to all clients listening for a job.
+
+    This wakes up all waiting SSE generators via the event signal,
+    avoiding busy-wait polling.
+    """
     with _sse_lock:
         queues = _sse_queues.get(job_id, [])
         for q in queues:
             q.append(data)
 
+        # Update last activity timestamp
+        _sse_timestamps[job_id] = time.time()
+
+        # Signal waiting threads that new data is available
+        if job_id in _sse_events:
+            _sse_events[job_id].set()
+
 
 def _make_analysis_callback(
     job_id: str,
@@ -187,6 +226,9 @@ def run_upload() -> None:
 def get_progress(job_id: str) -> Response:
     """Stream progress updates for a job via Server-Sent Events.
 
+    Uses event-driven signaling (instead of polling) and periodic heartbeats
+    to efficiently detect client disconnects.
+
     Args:
         job_id: The job ID to monitor
 
@@ -196,12 +238,19 @@ def get_progress(job_id: str) -> Response:
     manager = get_upload_manager()
 
     def generate() -> Generator[str, None, None]:
-        # Create a queue for this client
+        # Create a queue for this client and an event for signaling
         queue: deque[dict[str, Any]] = deque()
+        event = threading.Event()
+
         with _sse_lock:
             if job_id not in _sse_queues:
                 _sse_queues[job_id] = []
             _sse_queues[job_id].append(queue)
+            _sse_events[job_id] = event
+            _sse_timestamps[job_id] = time.time()
+
+        # Periodic cleanup of old queues
+        _cleanup_old_sse_queues()
 
         try:
             # Send initial state
@@ -216,15 +265,33 @@ def generate() -> Generator[str, None, None]:
                     yield f"data: {json.dumps(job.to_dict())}\n\n"
                 else:
                     yield f"data: {json.dumps(job.to_progress_dict())}\n\n"
+                    # Replay per-file states for files already past PENDING.
+                    # Covers the race window where ANALYZING events fired
+                    # before the EventSource connected.
+                    analysis_complete = job.status.value in ("ready", "failed")
+                    for fs in job.files:
+                        if fs.status != UploadStatus.PENDING:
+                            replay = {
+                                "type": "analysis_progress",
+                                "job_id": job.job_id,
+                                "job_status": job.status.value,
+                                "file": fs.to_dict(),
+                                "total_files": len(job.files),
+                                "analysis_complete": analysis_complete,
+                            }
+                            yield f"data: {json.dumps(replay)}\n\n"
             elif scan_job:
                 yield f"data: {json.dumps({'type': 'scan_initial', 'status': scan_job.status})}\n\n"
 
-            # Stream updates
+            last_heartbeat_time = time.time()
+
+            # Stream updates with event-driven waiting (no polling)
             while True:
-                # Check for updates
+                # Process all queued events
                 while queue:
                     data = queue.popleft()
                     yield f"data: {json.dumps(data)}\n\n"
+                    last_heartbeat_time = time.time()
 
                     # Check if job is complete (upload jobs)
                     if data.get("status") in ("completed", "failed", "cancelled"):
@@ -235,8 +302,15 @@ def generate() -> Generator[str, None, None]:
                         if not data.get("type"):
                             return
 
-                # Small delay to prevent busy waiting
-                time.sleep(0.1)
+                # Send heartbeat if no activity for a while
+                now = time.time()
+                if now - last_heartbeat_time > SSE_HEARTBEAT_INTERVAL_SECONDS:
+                    yield ": heartbeat\n\n"  # Comment line, ignored by EventSource
+                    last_heartbeat_time = now
+
+                # Wait for signal (blocking, no CPU waste) with timeout for heartbeat
+                event.wait(timeout=SSE_HEARTBEAT_INTERVAL_SECONDS)
+                event.clear()
 
                 # Check if job still exists (upload or scan)
                 job = manager.get_job(job_id)
@@ -281,12 +355,15 @@ def generate() -> Generator[str, None, None]:
                     return
 
         finally:
-            # Clean up queue
+            # Clean up queue and event
             with _sse_lock:
                 if job_id in _sse_queues and queue in _sse_queues[job_id]:
                     _sse_queues[job_id].remove(queue)
                     if not _sse_queues[job_id]:
-                        del _sse_queues[job_id]
+                        # Last client disconnected, remove event too
+                        _sse_queues.pop(job_id, None)
+                        _sse_events.pop(job_id, None)
+                        # Keep timestamp for TTL cleanup
 
     return Response(
         generate(),
@@ -318,6 +395,68 @@ def get_status(job_id: str) -> tuple[Response, int]:
     return jsonify(job.to_dict()), 200
 
 
+@upload_bp.route("/results/<job_id>", methods=["GET"])
+def get_results(job_id: str) -> tuple[Response, int]:
+    """Get paginated results for a completed job.
+
+    For large jobs (>1000 files), results are stored in database and retrieved
+    in pages to prevent memory overload and large response payloads.
+
+    Args:
+        job_id: The job ID to get results for
+
+    Query parameters:
+        page: Page number (default: 1)
+        per_page: Results per page (default: 100, max: 500)
+
+    Returns:
+        JSON response with paginated file results and job metadata
+    """
+    from app.services.job_storage import get_job_storage
+
+    manager = get_upload_manager()
+    storage = get_job_storage()
+
+    # Try to get from database first (for large jobs)
+    db_job = storage.get_job(job_id)
+    if db_job:
+        page = request.args.get("page", 1, type=int)
+        per_page = min(request.args.get("per_page", 100, type=int), 500)
+
+        results = storage.get_job_results(job_id, page=page, per_page=per_page)
+        results["job_metadata"] = db_job
+        return jsonify(results), 200
+
+    # Fall back to in-memory job (for small jobs)
+    job = manager.get_job(job_id)
+    if not job:
+        return jsonify({"error": "Job not found"}), 404
+
+    # Return in-memory job with all files (small jobs only)
+    return jsonify(
+        {
+            "job_id": job_id,
+            "files": [f.to_dict() for f in job.files],
+            "pagination": {
+                "page": 1,
+                "per_page": len(job.files),
+                "total_files": len(job.files),
+                "total_pages": 1,
+                "has_next": False,
+                "has_prev": False,
+            },
+            "job_metadata": {
+                "job_id": job.job_id,
+                "status": job.status.value,
+                "total_files": len(job.files),
+                "files_uploaded": sum(1 for f in job.files if f.status == UploadStatus.COMPLETED),
+                "files_failed": job.files_failed,
+                "total_bytes": job.total_bytes,
+            },
+        }
+    ), 200
+
+
 @upload_bp.route("/active", methods=["GET"])
 def get_active_job() -> tuple[Response, int]:
     """Get the most recent active job (for state restoration on page refresh).
@@ -345,6 +484,27 @@ def get_active_job() -> tuple[Response, int]:
         return jsonify({"job_id": None, "job": None}), 200
 
 
+@upload_bp.route("/cleanup-sse", methods=["POST"])
+def cleanup_sse_queues() -> tuple[Response, int]:
+    """Clean up stale SSE queues and events.
+
+    This can be called periodically or manually to reclaim memory from
+    abandoned connections. Returns the number of queues removed.
+
+    Returns:
+        JSON response with cleanup statistics
+    """
+    removed = _cleanup_old_sse_queues()
+    return jsonify(
+        {
+            "success": True,
+            "queues_removed": removed,
+            "active_queues": len(_sse_queues),
+            "ttl_seconds": SSE_QUEUE_TTL_SECONDS,
+        }
+    ), 200
+
+
 @upload_bp.route("/cancel/<job_id>", methods=["POST"])
 def cancel_upload(job_id: str) -> tuple[Response, int]:
     """Cancel an upload job.
@@ -538,8 +698,11 @@ def bulk_analyze() -> tuple[Response, int]:
             }
         ), 200
 
-    # When force-reuploading, analyze ALL files (not just non-duplicates)
-    job_files = file_paths if not skip_duplicates else files_to_analyze
+    # Always include all user-selected files in the job. The pipeline marks
+    # already-uploaded files as "skipped" when skip_duplicates=True rather than
+    # silently dropping them — an empty job_files here causes a 0-file job that
+    # completes instantly and bypasses the upload screen entirely.
+    job_files = file_paths
 
     # Create job with files that need analysis (no temp_dir - direct file access)
     job = manager.create_job(job_files, auto_upload=auto_upload)

From 6b38249787b736a18c9c2decccebae138d16a05e Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:07:33 -0700
Subject: [PATCH 145/173] Backend: Handle delete in batches

---
 app/services/delete_manager.py | 195 ++++++++++++++++++++++++++++++++-
 1 file changed, 189 insertions(+), 6 deletions(-)

diff --git a/app/services/delete_manager.py b/app/services/delete_manager.py
index f5d3b21..cbb8680 100644
--- a/app/services/delete_manager.py
+++ b/app/services/delete_manager.py
@@ -167,9 +167,24 @@ def is_multipart_etag(etag: str) -> bool:
 class DeleteManager:
     """Manages local file deletion jobs with MD5 verification against S3."""
 
-    def __init__(self) -> None:
+    def __init__(self, batch_config: dict[str, Any] | None = None) -> None:
         self.jobs: dict[str, DeleteJob] = {}
 
+        # Load batch processing configuration
+        if batch_config is None:
+            from app.config import get_settings
+
+            settings = get_settings()
+            batch_config = settings.get_batch_config()
+
+        # Import BatchConfig and BatchProcessor
+        from app.services.batch_processor import BatchConfig, BatchProcessor
+
+        self.batch_config = BatchConfig.from_dict(batch_config)
+        self.batch_processor = (
+            BatchProcessor(self.batch_config) if self.batch_config.enabled else None
+        )
+
     def scan_folder(
         self,
         folder_path: str,
@@ -237,6 +252,7 @@ def start_delete_job(
         aws_profile: str,
         aws_region: str,
         progress_callback: Callable[[DeleteJob], None] | None = None,
+        batch_callback: Callable[[dict[str, Any]], None] | None = None,
     ) -> bool:
         """Start verification and deletion for a job.
 
@@ -249,6 +265,7 @@ def start_delete_job(
             aws_profile: AWS profile name
             aws_region: AWS region
             progress_callback: Called after each file status change
+            batch_callback: Called for batch-level events (batch_started, batch_completed)
 
         Returns:
             True if job was started
@@ -328,9 +345,7 @@ def verify_against_s3(file_state: FileDeleteState) -> None:
                 return
 
             try:
-                metadata = get_object_metadata(
-                    s3_client, file_state.s3_bucket, file_state.s3_path
-                )
+                metadata = get_object_metadata(s3_client, file_state.s3_bucket, file_state.s3_path)
                 if not metadata["success"]:
                     with job.lock:
                         file_state.status = DeleteStatus.FAILED
@@ -379,8 +394,50 @@ def verify_against_s3(file_state: FileDeleteState) -> None:
             if progress_callback:
                 progress_callback(job)
 
-        with ThreadPoolExecutor(max_workers=4) as executor:
-            executor.map(verify_against_s3, job.files)
+        # Phase 2: Verify files against S3
+        # Use batch processing for large jobs to improve performance and UI responsiveness
+        use_batch_processing = (
+            self.batch_processor is not None
+            and self.batch_processor.should_use_batch_processing(len(job.files))
+        )
+
+        if use_batch_processing and self.batch_processor:
+            log.info(
+                "delete",
+                "using_batch_processing",
+                f"Using batch processing for {len(job.files)} files",
+                {"job_id": job_id, "total_files": len(job.files)},
+            )
+
+            # Process verification in batches
+            def check_cancelled() -> bool:
+                return job.cancelled
+
+            # Create a wrapper that uses _verify_batch
+            def process_batch_fn(
+                batch_files: list[FileDeleteState], batch_id: int, total_batches: int
+            ) -> dict[str, Any]:
+                return self._verify_batch(
+                    batch_files,
+                    batch_id,
+                    total_batches,
+                    job,
+                    s3_client,
+                    progress_callback,
+                    batch_callback,
+                )
+
+            # Use batch processor
+            self.batch_processor.process_batches(
+                job.files,
+                process_batch_fn,
+                progress_callback=None,  # We handle progress in _verify_batch
+                check_cancelled=check_cancelled,
+            )
+        else:
+            # Traditional non-batch processing
+            with ThreadPoolExecutor(max_workers=4) as executor:
+                executor.map(verify_against_s3, job.files)
 
         if job.cancelled:
             self._finalize_cancelled(job, progress_callback)
@@ -451,6 +508,132 @@ def verify_against_s3(file_state: FileDeleteState) -> None:
 
         return True
 
+    def _verify_batch(
+        self,
+        batch_files: list[FileDeleteState],
+        batch_id: int,
+        total_batches: int,
+        job: DeleteJob,
+        s3_client: Any,
+        progress_callback: Callable[[DeleteJob], None] | None,
+        batch_callback: Callable[[dict[str, Any]], None] | None,
+    ) -> dict[str, Any]:
+        """Verify a batch of files against S3.
+
+        Args:
+            batch_files: Files to verify in this batch
+            batch_id: 0-indexed batch number
+            total_batches: Total number of batches
+            job: The delete job
+            s3_client: S3 client for HEAD requests
+            progress_callback: Called after each file verification
+            batch_callback: Called for batch-level events
+
+        Returns:
+            Dict with batch statistics
+        """
+        # Send batch_started event
+        if batch_callback:
+            batch_callback(
+                {
+                    "type": "batch_started",
+                    "batch_id": batch_id,
+                    "total_batches": total_batches,
+                    "files_in_batch": len(batch_files),
+                }
+            )
+
+        verified = 0
+        failed = 0
+
+        def verify_against_s3(file_state: FileDeleteState) -> None:
+            """Verify a file against S3 using HEAD + size (primary) and MD5 (secondary)."""
+            nonlocal verified, failed
+
+            if job.cancelled:
+                return
+            if file_state.status == DeleteStatus.FAILED:
+                failed += 1
+                return
+
+            try:
+                metadata = get_object_metadata(s3_client, file_state.s3_bucket, file_state.s3_path)
+                if not metadata["success"]:
+                    with job.lock:
+                        file_state.status = DeleteStatus.FAILED
+                        file_state.error_message = (
+                            f"S3 object not found: {metadata.get('error', 'unknown')}"
+                        )
+                    failed += 1
+                    return
+
+                s3_size = int(metadata["size"])
+                etag = str(metadata["etag"])
+                file_state.s3_etag = etag
+                file_state.s3_size = s3_size
+
+                # Primary check: file size must match
+                if s3_size != file_state.file_size:
+                    with job.lock:
+                        file_state.status = DeleteStatus.MISMATCH
+                        file_state.error_message = (
+                            f"Size mismatch: local={file_state.file_size}, s3={s3_size}"
+                        )
+                    failed += 1
+                    return
+
+                # Secondary check: MD5 vs ETag (only possible for single-part uploads)
+                if is_multipart_etag(etag):
+                    with job.lock:
+                        file_state.status = DeleteStatus.VERIFIED
+                        file_state.verification = "size"
+                    verified += 1
+                else:
+                    if etag == file_state.local_md5:
+                        with job.lock:
+                            file_state.status = DeleteStatus.VERIFIED
+                            file_state.verification = "md5+size"
+                        verified += 1
+                    else:
+                        with job.lock:
+                            file_state.status = DeleteStatus.MISMATCH
+                            file_state.error_message = (
+                                f"MD5 mismatch: local={file_state.local_md5}, s3={etag}"
+                            )
+                        failed += 1
+            except Exception as e:
+                with job.lock:
+                    file_state.status = DeleteStatus.FAILED
+                    file_state.error_message = f"S3 verification failed: {e}"
+                failed += 1
+
+            if progress_callback:
+                progress_callback(job)
+
+        # Process batch with ThreadPoolExecutor
+        max_workers = self.batch_config.max_workers if self.batch_processor else 4
+        with ThreadPoolExecutor(max_workers=max_workers) as executor:
+            executor.map(verify_against_s3, batch_files)
+
+        # Send batch_completed event
+        if batch_callback:
+            batch_callback(
+                {
+                    "type": "batch_completed",
+                    "batch_id": batch_id,
+                    "files_verified": verified,
+                    "files_failed": failed,
+                }
+            )
+
+        return {
+            "success": not job.cancelled,
+            "processed": len(batch_files),
+            "uploaded": verified,  # "uploaded" maps to "verified" for delete operations
+            "failed": failed,
+            "bytes_uploaded": 0,  # Not applicable for delete
+        }
+
     def _finalize_cancelled(
         self,
         job: DeleteJob,

From 5691b0b8efed43bf5b17f0cad2d2ebb79c9b0306 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:08:01 -0700
Subject: [PATCH 146/173] Backend: Add additional information to logs

---
 app/services/log_service.py | 138 +++++++++++++++++++-----------------
 1 file changed, 73 insertions(+), 65 deletions(-)

diff --git a/app/services/log_service.py b/app/services/log_service.py
index ba2a4d6..854be2c 100644
--- a/app/services/log_service.py
+++ b/app/services/log_service.py
@@ -42,11 +42,7 @@ def _get_hive_dir(self, subdir: str, dt: datetime) -> Path:
         """
         log_dir = self._get_log_dir()
         hive_dir = (
-            log_dir
-            / subdir
-            / f"year={dt.year:04d}"
-            / f"month={dt.month:02d}"
-            / f"day={dt.day:02d}"
+            log_dir / subdir / f"year={dt.year:04d}" / f"month={dt.month:02d}" / f"day={dt.day:02d}"
         )
         hive_dir.mkdir(parents=True, exist_ok=True)
         return hive_dir
@@ -211,22 +207,24 @@ def save_job_csv(
                 if duration and duration > 0
                 else None
             )
-            writer.writerow([
-                job_id,
-                f.filename,
-                f.file_size,
-                format_file_size(f.file_size),
-                f.s3_path,
-                f.status.value,
-                f.start_time.isoformat() if f.start_time else "",
-                f.upload_started_at.isoformat() if f.upload_started_at else "",
-                f.upload_completed_at.isoformat() if f.upload_completed_at else "",
-                f.upload_duration_seconds,
-                speed,
-                f.is_duplicate,
-                f.is_valid,
-                f.error_message,
-            ])
+            writer.writerow(
+                [
+                    job_id,
+                    f.filename,
+                    f.file_size,
+                    format_file_size(f.file_size),
+                    f.s3_path,
+                    f.status.value,
+                    f.start_time.isoformat() if f.start_time else "",
+                    f.upload_started_at.isoformat() if f.upload_started_at else "",
+                    f.upload_completed_at.isoformat() if f.upload_completed_at else "",
+                    f.upload_duration_seconds,
+                    speed,
+                    f.is_duplicate,
+                    f.is_valid,
+                    f.error_message,
+                ]
+            )
 
         with self._write_lock:
             with open(out_path, "w", encoding="utf-8", newline="") as fh:
@@ -251,28 +249,32 @@ def list_log_files(self) -> list[dict[str, Any]]:
             for f in sorted(json_dir.rglob("*.jsonl"), reverse=True):
                 date_str = self._extract_date_from_hive_path(f)
                 rel_path = f.relative_to(log_dir)
-                result.append({
-                    "date": date_str,
-                    "filename": f.name,
-                    "path": str(f),
-                    "relative_path": str(rel_path),
-                    "size_bytes": f.stat().st_size,
-                    "type": "jsonl",
-                })
+                result.append(
+                    {
+                        "date": date_str,
+                        "filename": f.name,
+                        "path": str(f),
+                        "relative_path": str(rel_path),
+                        "size_bytes": f.stat().st_size,
+                        "type": "jsonl",
+                    }
+                )
 
         # Collect CSV files under csv/
         if csv_dir.exists():
             for f in sorted(csv_dir.rglob("*.csv"), reverse=True):
                 date_str = self._extract_date_from_hive_path(f)
                 rel_path = f.relative_to(log_dir)
-                result.append({
-                    "date": date_str,
-                    "filename": f.name,
-                    "path": str(f),
-                    "relative_path": str(rel_path),
-                    "size_bytes": f.stat().st_size,
-                    "type": "csv",
-                })
+                result.append(
+                    {
+                        "date": date_str,
+                        "filename": f.name,
+                        "path": str(f),
+                        "relative_path": str(rel_path),
+                        "size_bytes": f.stat().st_size,
+                        "type": "csv",
+                    }
+                )
 
         return result
 
@@ -423,12 +425,14 @@ def get_log_stats(self) -> dict[str, Any]:
             for csv_file in sorted(csv_dir.rglob("*.csv"), reverse=True):
                 date_str = self._extract_date_from_hive_path(csv_file) or ""
                 rel_path = str(csv_file.relative_to(log_dir))
-                csv_files.append({
-                    "path": rel_path,
-                    "filename": csv_file.name,
-                    "date": date_str,
-                    "size": csv_file.stat().st_size,
-                })
+                csv_files.append(
+                    {
+                        "path": rel_path,
+                        "filename": csv_file.name,
+                        "date": date_str,
+                        "size": csv_file.stat().st_size,
+                    }
+                )
 
         return {
             "total_entries": total_entries,
@@ -511,14 +515,16 @@ def get_upload_stats(self) -> dict[str, Any]:
 
                         session_duration += duration
 
-                        session_files.append({
-                            "filename": row.get("filename", ""),
-                            "file_size_formatted": row.get("file_size_formatted", ""),
-                            "status": status,
-                            "upload_speed_mbps": speed,
-                            "s3_path": row.get("s3_path", ""),
-                            "error_message": row.get("error_message", ""),
-                        })
+                        session_files.append(
+                            {
+                                "filename": row.get("filename", ""),
+                                "file_size_formatted": row.get("file_size_formatted", ""),
+                                "status": status,
+                                "upload_speed_mbps": speed,
+                                "s3_path": row.get("s3_path", ""),
+                                "error_message": row.get("error_message", ""),
+                            }
+                        )
             except (OSError, csv.Error):
                 continue
 
@@ -531,20 +537,22 @@ def get_upload_stats(self) -> dict[str, Any]:
             if session_duration > 0 and session_bytes > 0:
                 avg_speed = round(session_bytes / session_duration / 1024 / 1024 * 8, 1)
 
-            sessions.append({
-                "csv_path": rel_path,
-                "date": date_str,
-                "time": time_str,
-                "total_files": len(session_files),
-                "completed": session_completed,
-                "failed": session_failed,
-                "skipped": session_skipped,
-                "total_bytes": session_bytes,
-                "total_bytes_formatted": format_file_size(session_bytes),
-                "total_duration_seconds": round(session_duration, 1),
-                "avg_speed_mbps": avg_speed,
-                "files": session_files,
-            })
+            sessions.append(
+                {
+                    "csv_path": rel_path,
+                    "date": date_str,
+                    "time": time_str,
+                    "total_files": len(session_files),
+                    "completed": session_completed,
+                    "failed": session_failed,
+                    "skipped": session_skipped,
+                    "total_bytes": session_bytes,
+                    "total_bytes_formatted": format_file_size(session_bytes),
+                    "total_duration_seconds": round(session_duration, 1),
+                    "avg_speed_mbps": avg_speed,
+                    "files": session_files,
+                }
+            )
 
         return {
             "total_files_uploaded": total_uploaded,

From 7c43ebc93abcb2678e74d8689c7e5d1c9c69d491 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:08:53 -0700
Subject: [PATCH 147/173] Backend: Extract mcap dates from filename in "fast
 mode"

---
 app/services/mcap_service.py | 55 ++++++++++++++++++++++++++++++------
 1 file changed, 47 insertions(+), 8 deletions(-)

diff --git a/app/services/mcap_service.py b/app/services/mcap_service.py
index 705d7c6..40e622a 100644
--- a/app/services/mcap_service.py
+++ b/app/services/mcap_service.py
@@ -163,15 +163,50 @@ def _find_datetime_in_dataframes(dataframes: dict[str, pd.DataFrame]) -> datetim
     return earliest_time
 
 
-def extract_start_time(file_path: Path | str) -> datetime:
-    """Extract the earliest timestamp from an MCAP file using modaq_toolkit.
+def extract_start_time_fast(file_path: Path | str) -> datetime:
+    """Extract timestamp from filename only (skip MCAP parsing for speed).
+
+    This is a fast path that extracts timestamps solely from the filename,
+    skipping the expensive MCAP parsing step. Use when you trust your
+    filenames are correctly formatted and want maximum performance.
+
+    Performance: ~0.1ms vs ~200ms for full MCAP parsing (2000x speedup)
+
+    Args:
+        file_path: Path to the MCAP file
+
+    Returns:
+        datetime: The timestamp extracted from the filename
+
+    Raises:
+        ValueError: If timestamp cannot be extracted from filename
+        FileNotFoundError: If the file does not exist
+    """
+    path = Path(file_path)
+    if not path.exists():
+        raise FileNotFoundError(f"MCAP file not found: {path}")
+
+    timestamp = _extract_timestamp_from_filename(path.name)
+    if timestamp is None:
+        raise ValueError(
+            f"Cannot extract timestamp from filename: {path.name}. "
+            "Consider using extract_start_time() for full MCAP parsing."
+        )
+
+    return timestamp
+
+
+def extract_start_time(file_path: Path | str, skip_validation: bool = False) -> datetime:
+    """Extract the earliest timestamp from an MCAP file.
 
     Tries multiple strategies:
-    1. Parse MCAP file and look for datetime indices/columns
-    2. Extract timestamp from filename if MCAP parsing fails or returns invalid dates
+    1. If skip_validation=True: Extract from filename only (fast path)
+    2. If skip_validation=False: Parse MCAP file and look for datetime indices/columns
+    3. Fallback: Extract timestamp from filename if MCAP parsing fails
 
     Args:
         file_path: Path to the MCAP file
+        skip_validation: If True, skip MCAP parsing and extract from filename only
 
     Returns:
         datetime: The earliest timestamp found in the MCAP file
@@ -180,6 +215,9 @@ def extract_start_time(file_path: Path | str) -> datetime:
         ValueError: If the file cannot be parsed or has no timestamps
         FileNotFoundError: If the file does not exist
     """
+    # Fast path: skip MCAP validation
+    if skip_validation:
+        return extract_start_time_fast(file_path)
     from modaq_toolkit import MCAPParser
 
     path = Path(file_path)
@@ -262,11 +300,14 @@ def generate_s3_path(start_time: datetime, filename: str) -> str:
     return path
 
 
-def get_file_info(file_path: Path | str) -> dict[str, str | int | None]:
+def get_file_info(
+    file_path: Path | str, skip_validation: bool = False
+) -> dict[str, str | int | None]:
     """Get information about an MCAP file.
 
     Args:
         file_path: Path to the MCAP file
+        skip_validation: If True, skip MCAP parsing and extract from filename only
 
     Returns:
         Dictionary containing file information
@@ -283,12 +324,10 @@ def get_file_info(file_path: Path | str) -> dict[str, str | int | None]:
     }
 
     try:
-        start_time = extract_start_time(path)
+        start_time = extract_start_time(path, skip_validation=skip_validation)
         info["start_time"] = start_time.isoformat()
         info["s3_path"] = generate_s3_path(start_time, path.name)
     except Exception as e:
         info["error"] = str(e)
 
     return info
-
-

From acadc65f90bf43d552b17aa84c23374a147f0a79 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:10:45 -0700
Subject: [PATCH 148/173] Backend: Refactor upload with skip validation and
 more correct pending logic

---
 app/services/s3_service.py     |   1 +
 app/services/upload_manager.py | 519 +++++++++++++++++++--------------
 2 files changed, 306 insertions(+), 214 deletions(-)

diff --git a/app/services/s3_service.py b/app/services/s3_service.py
index 362e3a1..f1afa60 100644
--- a/app/services/s3_service.py
+++ b/app/services/s3_service.py
@@ -14,6 +14,7 @@
 class UploadCancelledError(Exception):
     """Raised when an upload is cancelled mid-transfer."""
 
+
 # Multipart threshold: files below this size are uploaded as a single PUT request,
 # which produces a simple MD5 ETag. Files above use multipart upload, which produces
 # a composite ETag (md5_of_part_md5s-part_count) that can't be compared to a local MD5.
diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index b8e7fd9..849b9bb 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -6,7 +6,13 @@
 import threading
 import uuid
 from collections.abc import Callable
-from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
+from concurrent.futures import (
+    FIRST_COMPLETED,
+    ProcessPoolExecutor,
+    ThreadPoolExecutor,
+    as_completed,
+    wait,
+)
 from dataclasses import dataclass, field
 from datetime import UTC, datetime
 from enum import Enum
@@ -25,14 +31,18 @@
 EPOCH_CUTOFF = datetime(1980, 1, 1, tzinfo=UTC)
 
 
-def _extract_start_time_worker(local_path: str) -> datetime | str:
+def _extract_start_time_worker(local_path: str, skip_validation: bool = False) -> datetime | str:
     """Worker function for ProcessPoolExecutor — must be top-level for pickling.
 
+    Args:
+        local_path: Path to the MCAP file
+        skip_validation: If True, skip MCAP parsing and extract from filename only
+
     Returns:
         datetime on success, or error message string on failure.
     """
     try:
-        return mcap_service.extract_start_time(local_path)
+        return mcap_service.extract_start_time(local_path, skip_validation=skip_validation)
     except Exception as e:
         return str(e)
 
@@ -304,12 +314,27 @@ class ScanJob:
 class UploadManager:
     """Manages upload jobs and their execution."""
 
-    def __init__(self, max_workers: int = 4) -> None:
+    def __init__(self, max_workers: int = 4, batch_config: dict[str, Any] | None = None) -> None:
         self.jobs: dict[str, UploadJob] = {}
         self.scan_jobs: dict[str, ScanJob] = {}
         self.max_workers = max_workers
         self._lock = threading.Lock()
 
+        # Load batch processing configuration
+        if batch_config is None:
+            from app.config import get_settings
+
+            settings = get_settings()
+            batch_config = settings.get_batch_config()
+
+        # Import BatchConfig and BatchProcessor
+        from app.services.batch_processor import BatchConfig, BatchProcessor
+
+        self.batch_config = BatchConfig.from_dict(batch_config)
+        self.batch_processor = (
+            BatchProcessor(self.batch_config) if self.batch_config.enabled else None
+        )
+
     def create_job(
         self,
         file_paths: list[str],
@@ -367,6 +392,7 @@ def analyze_job(
         aws_profile: str,
         aws_region: str,
         s3_bucket: str,
+        skip_validation: bool | None = None,
     ) -> UploadJob | None:
         """Analyze files in a job - extract timestamps and check for duplicates.
 
@@ -375,10 +401,17 @@ def analyze_job(
             aws_profile: AWS profile to use
             aws_region: AWS region
             s3_bucket: S3 bucket to check for duplicates
+            skip_validation: If True, skip MCAP parsing. If None, use live settings.
 
         Returns:
             The updated UploadJob or None if not found
         """
+        if skip_validation is None:
+            from app.config import get_settings
+
+            skip_validation = bool(
+                get_settings().batch_processing.get("skip_mcap_validation", False)
+            )
         job = self.get_job(job_id)
         if not job:
             return None
@@ -400,7 +433,9 @@ def analyze_job(
             file_state.status = UploadStatus.ANALYZING
             try:
                 # Extract timestamp from MCAP
-                start_time = mcap_service.extract_start_time(file_state.local_path)
+                start_time = mcap_service.extract_start_time(
+                    file_state.local_path, skip_validation=skip_validation
+                )
                 file_state.start_time = start_time
 
                 # Generate S3 path
@@ -463,6 +498,7 @@ def _analyze_single_file(
         job_id: str = "",
         progress_callback: Callable[["UploadJob", FileUploadState], None] | None = None,
         job: "UploadJob | None" = None,
+        skip_validation: bool = False,
     ) -> FileUploadState:
         """Analyze a single file - extract timestamp and check for duplicates.
 
@@ -474,6 +510,7 @@ def _analyze_single_file(
             job_id: The parent job ID (for logging)
             progress_callback: Optional callback fired when file starts analyzing
             job: The parent UploadJob (needed for callback)
+            skip_validation: If True, skip MCAP parsing and extract from filename only
 
         Returns:
             The updated FileUploadState
@@ -484,7 +521,9 @@ def _analyze_single_file(
             progress_callback(job, file_state)
         try:
             # Extract timestamp from MCAP
-            start_time = mcap_service.extract_start_time(file_state.local_path)
+            start_time = mcap_service.extract_start_time(
+                file_state.local_path, skip_validation=skip_validation
+            )
             file_state.start_time = start_time
 
             # Check if timestamp is valid (after 1980)
@@ -557,6 +596,7 @@ def analyze_job_async(
         s3_bucket: str,
         progress_callback: Callable[["UploadJob", FileUploadState], None] | None = None,
         use_cache: bool = True,
+        skip_validation: bool | None = None,
     ) -> UploadJob | None:
         """Analyze files in a job asynchronously with parallel processing.
 
@@ -567,10 +607,17 @@ def analyze_job_async(
             s3_bucket: S3 bucket to check for duplicates
             progress_callback: Optional callback called after each file completes
             use_cache: Whether to use cache for duplicate checking
+            skip_validation: If True, skip MCAP parsing. If None, use live settings.
 
         Returns:
             The updated UploadJob or None if not found
         """
+        if skip_validation is None:
+            from app.config import get_settings
+
+            skip_validation = bool(
+                get_settings().batch_processing.get("skip_mcap_validation", False)
+            )
         log = get_log_service()
         job = self.get_job(job_id)
         if not job:
@@ -601,38 +648,55 @@ def analyze_job_async(
         # parallelism across cores, bypassing the GIL.
         cpu_workers = max(1, (os.cpu_count() or 4) - 1)
         for file_state in job.files:
-            file_state.status = UploadStatus.ANALYZING
+            file_state.status = UploadStatus.PENDING
+
+        files_iter_async = iter(job.files)
+        active_async: dict[Any, FileUploadState] = {}
+
+        def _submit_next_async(proc_executor: ProcessPoolExecutor) -> None:
+            fs = next(files_iter_async, None)
+            if fs is None or job.cancelled:
+                return
+            fs.status = UploadStatus.ANALYZING
+            if progress_callback:
+                progress_callback(job, fs)  # "queued → analyzing" event
+            fut = proc_executor.submit(_extract_start_time_worker, fs.local_path, skip_validation)
+            active_async[fut] = fs
 
         with ProcessPoolExecutor(max_workers=cpu_workers) as proc_executor:
-            parse_futures = {
-                proc_executor.submit(_extract_start_time_worker, file_state.local_path): file_state
-                for file_state in job.files
-            }
-            for future in as_completed(parse_futures):
+            for _ in range(cpu_workers):
+                _submit_next_async(proc_executor)
+
+            while active_async:
                 if job.cancelled:
-                    for pending_future in parse_futures:
-                        pending_future.cancel()
+                    for f in list(active_async.keys()):
+                        f.cancel()
                     break
 
-                file_state = parse_futures[future]
-                result = future.result()
-                if isinstance(result, str):
-                    # Error message returned from worker
-                    file_state.status = UploadStatus.FAILED
-                    file_state.error_message = result
-                    log.error(
-                        "analysis",
-                        "file_analysis_failed",
-                        f"Failed to analyze {file_state.filename}: {result}",
-                        {"job_id": job_id, "filename": file_state.filename, "error": result},
-                    )
-                else:
-                    file_state.start_time = result
-                    naive_start = mcap_service.to_naive_utc(result)
-                    file_state.is_valid = naive_start >= EPOCH_CUTOFF.replace(tzinfo=None)
-                    file_state.s3_path = mcap_service.generate_s3_path(result, file_state.filename)
-                if progress_callback:
-                    progress_callback(job, file_state)
+                done, _ = wait(list(active_async.keys()), return_when=FIRST_COMPLETED)
+                for future in done:
+                    file_state = active_async.pop(future)
+                    result = future.result()
+                    if isinstance(result, str):
+                        # Error message returned from worker
+                        file_state.status = UploadStatus.FAILED
+                        file_state.error_message = result
+                        log.error(
+                            "analysis",
+                            "file_analysis_failed",
+                            f"Failed to analyze {file_state.filename}: {result}",
+                            {"job_id": job_id, "filename": file_state.filename, "error": result},
+                        )
+                    else:
+                        file_state.start_time = result
+                        naive_start = mcap_service.to_naive_utc(result)
+                        file_state.is_valid = naive_start >= EPOCH_CUTOFF.replace(tzinfo=None)
+                        file_state.s3_path = mcap_service.generate_s3_path(
+                            result, file_state.filename
+                        )
+                    if progress_callback:
+                        progress_callback(job, file_state)
+                    _submit_next_async(proc_executor)
 
         # Phase 2: S3 duplicate checks (I/O-bound) — threads are fine here.
         parsed_files = [f for f in job.files if f.status != UploadStatus.FAILED]
@@ -990,6 +1054,7 @@ def analyze_and_upload_pipeline(
         analysis_callback: Callable[["UploadJob", FileUploadState], None] | None = None,
         upload_callback: Callable[["UploadJob"], None] | None = None,
         use_cache: bool = True,
+        skip_validation: bool | None = None,
     ) -> None:
         """Analyze each file and upload it immediately — pipeline approach.
 
@@ -1007,7 +1072,17 @@ def analyze_and_upload_pipeline(
             analysis_callback: Called after each file is analyzed
             upload_callback: Called for upload progress updates
             use_cache: Whether to use cache for duplicate checking
+            skip_validation: If True, skip MCAP parsing. If None, use batch_config setting
         """
+        # Determine skip_validation setting — read live from settings so that
+        # changes made in the Settings UI take effect without a server restart.
+        # (UploadManager is a singleton whose batch_config is frozen at init time.)
+        if skip_validation is None:
+            from app.config import get_settings
+
+            skip_validation = bool(
+                get_settings().batch_processing.get("skip_mcap_validation", False)
+            )
         log = get_log_service()
         job = self.get_job(job_id)
         if not job:
@@ -1040,233 +1115,249 @@ def analyze_and_upload_pipeline(
         cpu_workers = max(1, (os.cpu_count() or 4) - 1)
         upload_executor = ThreadPoolExecutor(max_workers=self.max_workers)
 
-        # Set all files to ANALYZING
+        # Mark all files as PENDING (waiting their turn in the analysis pool)
         for fs in job.files:
+            fs.status = UploadStatus.PENDING
+
+        files_iter = iter(job.files)
+        active: dict[Any, FileUploadState] = {}
+
+        def _submit_next(proc_executor: ProcessPoolExecutor) -> None:
+            fs = next(files_iter, None)
+            if fs is None or job.cancelled:
+                return
             fs.status = UploadStatus.ANALYZING
+            if analysis_callback:
+                analysis_callback(job, fs)  # "queued → analyzing" event
+            fut = proc_executor.submit(_extract_start_time_worker, fs.local_path, skip_validation)
+            active[fut] = fs
 
         try:
-            # Submit all files for MCAP parsing (CPU-bound, true parallelism)
             with ProcessPoolExecutor(max_workers=cpu_workers) as proc_executor:
-                parse_futures = {
-                    proc_executor.submit(_extract_start_time_worker, fs.local_path): fs
-                    for fs in job.files
-                }
+                # Fill initial slots
+                for _ in range(cpu_workers):
+                    _submit_next(proc_executor)
 
-                for future in as_completed(parse_futures):
+                while active:
                     if job.cancelled:
-                        # Cancel remaining parse futures that haven't started yet
-                        for pending_future in parse_futures:
-                            pending_future.cancel()
+                        for f in list(active.keys()):
+                            f.cancel()
                         break
 
-                    fs = parse_futures[future]
-                    result = future.result()
-
-                    if isinstance(result, str):
-                        # Parse failed
-                        fs.status = UploadStatus.FAILED
-                        fs.error_message = result
-                        log.error(
-                            "analysis",
-                            "file_analysis_failed",
-                            f"Failed to analyze {fs.filename}: {result}",
-                            {"job_id": job_id, "filename": fs.filename, "error": result},
-                        )
-                        if analysis_callback:
-                            analysis_callback(job, fs)
-                        continue
-
-                    # Parse succeeded — set timestamp and generate S3 path
-                    fs.start_time = result
-                    naive_start = mcap_service.to_naive_utc(result)
-                    fs.is_valid = naive_start >= EPOCH_CUTOFF.replace(tzinfo=None)
-                    fs.s3_path = mcap_service.generate_s3_path(result, fs.filename)
-
-                    # Check duplicate (I/O but fast — cache lookup or S3 HEAD)
-                    self._check_duplicate(fs, s3_client, s3_bucket, use_cache)
-                    fs.status = UploadStatus.READY
-
-                    log.info(
-                        "analysis",
-                        "file_analysis_completed",
-                        f"Analyzed {fs.filename}",
-                        {
-                            "job_id": job_id,
-                            "filename": fs.filename,
-                            "file_size": fs.file_size,
-                            "s3_path": fs.s3_path,
-                            "is_duplicate": fs.is_duplicate,
-                            "is_valid": fs.is_valid,
-                        },
-                    )
+                    done, _ = wait(list(active.keys()), return_when=FIRST_COMPLETED)
+                    for future in done:
+                        fs = active.pop(future)
+                        result = future.result()
+
+                        if isinstance(result, str):
+                            # Parse failed
+                            fs.status = UploadStatus.FAILED
+                            fs.error_message = result
+                            log.error(
+                                "analysis",
+                                "file_analysis_failed",
+                                f"Failed to analyze {fs.filename}: {result}",
+                                {"job_id": job_id, "filename": fs.filename, "error": result},
+                            )
+                            if analysis_callback:
+                                analysis_callback(job, fs)
+                            _submit_next(proc_executor)
+                            continue
 
-                    # Notify frontend of analysis result
-                    if analysis_callback:
-                        analysis_callback(job, fs)
+                        # Parse succeeded — set timestamp and generate S3 path
+                        fs.start_time = result
+                        naive_start = mcap_service.to_naive_utc(result)
+                        fs.is_valid = naive_start >= EPOCH_CUTOFF.replace(tzinfo=None)
+                        fs.s3_path = mcap_service.generate_s3_path(result, fs.filename)
 
-                    # Decide: skip or upload?
-                    if not fs.is_valid:
-                        fs.status = UploadStatus.SKIPPED
-                        fs.error_message = "Invalid timestamp (pre-1980)"
-                        log.warning(
-                            "upload",
-                            "file_upload_skipped",
-                            f"Skipped invalid timestamp: {fs.filename}",
-                            {
-                                "job_id": job_id,
-                                "filename": fs.filename,
-                                "reason": "invalid_timestamp",
-                            },
-                        )
-                        if upload_callback:
-                            upload_callback(job)
-                        continue
+                        # Check duplicate (I/O but fast — cache lookup or S3 HEAD)
+                        self._check_duplicate(fs, s3_client, s3_bucket, use_cache)
+                        fs.status = UploadStatus.READY
 
-                    if skip_duplicates and fs.is_duplicate:
-                        fs.status = UploadStatus.SKIPPED
-                        fs.bytes_uploaded = fs.file_size
                         log.info(
-                            "upload",
-                            "file_upload_skipped",
-                            f"Skipped duplicate: {fs.filename}",
+                            "analysis",
+                            "file_analysis_completed",
+                            f"Analyzed {fs.filename}",
                             {
                                 "job_id": job_id,
                                 "filename": fs.filename,
-                                "reason": "duplicate",
+                                "file_size": fs.file_size,
+                                "s3_path": fs.s3_path,
+                                "is_duplicate": fs.is_duplicate,
+                                "is_valid": fs.is_valid,
                             },
                         )
-                        if upload_callback:
-                            upload_callback(job)
-                        continue
-
-                    # Submit for upload immediately
-                    def make_upload_task(
-                        file_state: FileUploadState,
-                    ) -> Callable[[], Any]:
-                        def upload_task() -> Any:
-                            if job.cancelled:
-                                with job.lock:
-                                    file_state.status = UploadStatus.CANCELLED
-                                if analysis_callback:
-                                    analysis_callback(job, file_state)
-                                if upload_callback:
-                                    upload_callback(job)
-                                return None
 
-                            try:
-                                with job.lock:
-                                    file_state.status = UploadStatus.UPLOADING
-                                    file_state.upload_started_at = datetime.now(UTC)
-                                log.info(
-                                    "upload",
-                                    "file_upload_started",
-                                    f"Uploading {file_state.filename}",
-                                    {
-                                        "job_id": job_id,
-                                        "filename": file_state.filename,
-                                        "file_size": file_state.file_size,
-                                        "s3_path": file_state.s3_path,
-                                    },
-                                )
-                                if upload_callback:
-                                    upload_callback(job)
+                        # Notify frontend of analysis result
+                        if analysis_callback:
+                            analysis_callback(job, fs)
 
-                                def byte_callback(uploaded: int, total: int) -> None:
+                        # Fill freed slot immediately
+                        _submit_next(proc_executor)
+
+                        # Decide: skip or upload?
+                        if not fs.is_valid:
+                            fs.status = UploadStatus.SKIPPED
+                            fs.error_message = "Invalid timestamp (pre-1980)"
+                            log.warning(
+                                "upload",
+                                "file_upload_skipped",
+                                f"Skipped invalid timestamp: {fs.filename}",
+                                {
+                                    "job_id": job_id,
+                                    "filename": fs.filename,
+                                    "reason": "invalid_timestamp",
+                                },
+                            )
+                            if upload_callback:
+                                upload_callback(job)
+                            continue
+
+                        if skip_duplicates and fs.is_duplicate:
+                            fs.status = UploadStatus.SKIPPED
+                            fs.bytes_uploaded = fs.file_size
+                            log.info(
+                                "upload",
+                                "file_upload_skipped",
+                                f"Skipped duplicate: {fs.filename}",
+                                {
+                                    "job_id": job_id,
+                                    "filename": fs.filename,
+                                    "reason": "duplicate",
+                                },
+                            )
+                            if upload_callback:
+                                upload_callback(job)
+                            continue
+
+                        # Submit for upload immediately
+                        def make_upload_task(
+                            file_state: FileUploadState,
+                        ) -> Callable[[], Any]:
+                            def upload_task() -> Any:
+                                if job.cancelled:
                                     with job.lock:
-                                        file_state.bytes_uploaded = uploaded
+                                        file_state.status = UploadStatus.CANCELLED
+                                    if analysis_callback:
+                                        analysis_callback(job, file_state)
                                     if upload_callback:
                                         upload_callback(job)
+                                    return None
 
-                                upload_result = s3_service.upload_file_with_progress(
-                                    s3_client,
-                                    file_state.local_path,
-                                    s3_bucket,
-                                    file_state.s3_path,
-                                    byte_callback,
-                                    cancel_check=lambda: job.cancelled,
-                                )
-
-                                # Handle completion inline
-                                file_state.upload_completed_at = datetime.now(UTC)
-                                if upload_result["success"]:
-                                    file_state.status = UploadStatus.COMPLETED
-                                    file_state.bytes_uploaded = file_state.file_size
+                                try:
+                                    with job.lock:
+                                        file_state.status = UploadStatus.UPLOADING
+                                        file_state.upload_started_at = datetime.now(UTC)
                                     log.info(
                                         "upload",
-                                        "file_upload_completed",
-                                        f"Uploaded {file_state.filename}",
+                                        "file_upload_started",
+                                        f"Uploading {file_state.filename}",
                                         {
                                             "job_id": job_id,
                                             "filename": file_state.filename,
                                             "file_size": file_state.file_size,
-                                            "upload_duration_seconds": (
-                                                file_state.upload_duration_seconds
-                                            ),
                                             "s3_path": file_state.s3_path,
                                         },
                                     )
-                                    try:
-                                        cache = get_cache_service()
-                                        cache.update_cache(
-                                            s3_bucket,
-                                            file_state.s3_path,
-                                            exists=True,
-                                            filename=file_state.filename,
-                                            file_size=file_state.file_size,
+                                    if upload_callback:
+                                        upload_callback(job)
+
+                                    def byte_callback(uploaded: int, total: int) -> None:
+                                        with job.lock:
+                                            file_state.bytes_uploaded = uploaded
+                                        if upload_callback:
+                                            upload_callback(job)
+
+                                    upload_result = s3_service.upload_file_with_progress(
+                                        s3_client,
+                                        file_state.local_path,
+                                        s3_bucket,
+                                        file_state.s3_path,
+                                        byte_callback,
+                                        cancel_check=lambda: job.cancelled,
+                                    )
+
+                                    # Handle completion inline
+                                    file_state.upload_completed_at = datetime.now(UTC)
+                                    if upload_result["success"]:
+                                        file_state.status = UploadStatus.COMPLETED
+                                        file_state.bytes_uploaded = file_state.file_size
+                                        log.info(
+                                            "upload",
+                                            "file_upload_completed",
+                                            f"Uploaded {file_state.filename}",
+                                            {
+                                                "job_id": job_id,
+                                                "filename": file_state.filename,
+                                                "file_size": file_state.file_size,
+                                                "upload_duration_seconds": (
+                                                    file_state.upload_duration_seconds
+                                                ),
+                                                "s3_path": file_state.s3_path,
+                                            },
+                                        )
+                                        try:
+                                            cache = get_cache_service()
+                                            cache.update_cache(
+                                                s3_bucket,
+                                                file_state.s3_path,
+                                                exists=True,
+                                                filename=file_state.filename,
+                                                file_size=file_state.file_size,
+                                            )
+                                        except Exception:
+                                            logger.debug(
+                                                "Cache update failed after upload",
+                                                exc_info=True,
+                                            )
+                                    else:
+                                        file_state.status = UploadStatus.FAILED
+                                        file_state.error_message = upload_result.get(
+                                            "error", "Unknown error"
                                         )
-                                    except Exception:
-                                        logger.debug(
-                                            "Cache update failed after upload",
-                                            exc_info=True,
+                                        log.error(
+                                            "upload",
+                                            "file_upload_failed",
+                                            f"Failed to upload {file_state.filename}: "
+                                            f"{file_state.error_message}",
+                                            {
+                                                "job_id": job_id,
+                                                "filename": file_state.filename,
+                                                "error": file_state.error_message,
+                                            },
                                         )
-                                else:
+                                except UploadCancelledError:
+                                    with job.lock:
+                                        file_state.status = UploadStatus.CANCELLED
+                                        file_state.upload_completed_at = datetime.now(UTC)
+                                except Exception as e:
+                                    file_state.upload_completed_at = datetime.now(UTC)
                                     file_state.status = UploadStatus.FAILED
-                                    file_state.error_message = upload_result.get(
-                                        "error", "Unknown error"
-                                    )
+                                    file_state.error_message = str(e)
                                     log.error(
                                         "upload",
                                         "file_upload_failed",
-                                        f"Failed to upload {file_state.filename}: "
-                                        f"{file_state.error_message}",
+                                        f"Failed to upload {file_state.filename}: {e}",
                                         {
                                             "job_id": job_id,
                                             "filename": file_state.filename,
-                                            "error": file_state.error_message,
+                                            "error": str(e),
                                         },
                                     )
-                            except UploadCancelledError:
-                                with job.lock:
-                                    file_state.status = UploadStatus.CANCELLED
-                                    file_state.upload_completed_at = datetime.now(UTC)
-                            except Exception as e:
-                                file_state.upload_completed_at = datetime.now(UTC)
-                                file_state.status = UploadStatus.FAILED
-                                file_state.error_message = str(e)
-                                log.error(
-                                    "upload",
-                                    "file_upload_failed",
-                                    f"Failed to upload {file_state.filename}: {e}",
-                                    {
-                                        "job_id": job_id,
-                                        "filename": file_state.filename,
-                                        "error": str(e),
-                                    },
-                                )
-
-                            # Notify per-file status so the frontend
-                            # updates this row immediately (the progress
-                            # dict only includes active files, so without
-                            # this the row would keep spinning).
-                            if analysis_callback:
-                                analysis_callback(job, file_state)
-                            if upload_callback:
-                                upload_callback(job)
-                            return None
 
-                        return upload_task
+                                # Notify per-file status so the frontend
+                                # updates this row immediately (the progress
+                                # dict only includes active files, so without
+                                # this the row would keep spinning).
+                                if analysis_callback:
+                                    analysis_callback(job, file_state)
+                                if upload_callback:
+                                    upload_callback(job)
+                                return None
+
+                            return upload_task
 
-                    upload_executor.submit(make_upload_task(fs))
+                        upload_executor.submit(make_upload_task(fs))
 
         except Exception as e:
             log.error(

From 8e001167ea71f3d22b5a740459904c694d571001 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:12:03 -0700
Subject: [PATCH 149/173] Frontend: Add hook support for folder scanStart

---
 frontend/src/hooks/useFolderScan.ts | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/frontend/src/hooks/useFolderScan.ts b/frontend/src/hooks/useFolderScan.ts
index 2308003..c54e413 100644
--- a/frontend/src/hooks/useFolderScan.ts
+++ b/frontend/src/hooks/useFolderScan.ts
@@ -12,6 +12,7 @@ import { useUploadStore } from "../stores/uploadStore.ts";
 import type {
   ScannedFolder,
   ScanEvent,
+  ScanStartedEvent,
   ScanFolderCompleteEvent,
   ScanCompleteEvent,
 } from "../types/api.ts";
@@ -32,6 +33,7 @@ interface UseFolderScanResult {
   startScan: (folderPath: string, cacheOnly?: boolean, exclusions?: ScanExclusions) => Promise<void>;
   cancelScan: () => Promise<void>;
   folders: ScannedFolder[];
+  foldersTotal: number;
   isScanning: boolean;
   scanComplete: boolean;
   totals: ScanTotals;
@@ -44,11 +46,13 @@ export function useFolderScan(): UseFolderScanResult {
     scanFolders: folders,
     isScanning,
     scanComplete,
+    scanFoldersTotal: foldersTotal,
     scanTotals: totals,
     setScanJobId,
     addScanFolder,
     setScanComplete,
     setIsScanning,
+    setScanFoldersTotal,
     updateScanTotals,
   } = useUploadStore();
 
@@ -59,9 +63,11 @@ export function useFolderScan(): UseFolderScanResult {
       if (!data || typeof data !== "object") return;
 
       switch (data.type) {
-        case "scan_started":
-          // Just update scanning state — we already set it in startScan.
+        case "scan_started": {
+          const evt = data as ScanStartedEvent;
+          setScanFoldersTotal(evt.folders_total);
           break;
+        }
 
         case "scan_folder_complete": {
           const evt = data as ScanFolderCompleteEvent;
@@ -88,7 +94,7 @@ export function useFolderScan(): UseFolderScanResult {
         }
       }
     },
-    [addScanFolder, updateScanTotals, setScanComplete, setIsScanning],
+    [addScanFolder, updateScanTotals, setScanComplete, setIsScanning, setScanFoldersTotal],
   );
 
   // Only connect when we have a jobId and are still scanning.
@@ -151,5 +157,5 @@ export function useFolderScan(): UseFolderScanResult {
     setJobId(null);
   }, [setIsScanning, setScanComplete]);
 
-  return { startScan, cancelScan, folders, isScanning, scanComplete, totals };
+  return { startScan, cancelScan, folders, foldersTotal, isScanning, scanComplete, totals };
 }

From 41381b6719b93b2596e082a8c284750ad1ae612f Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:15:03 -0700
Subject: [PATCH 150/173] Front: Update useSSE with heartbeat detection

---
 frontend/src/hooks/useSSE.ts | 37 ++++++++++++++++++++++++++++++++----
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/frontend/src/hooks/useSSE.ts b/frontend/src/hooks/useSSE.ts
index cce1988..b28039a 100644
--- a/frontend/src/hooks/useSSE.ts
+++ b/frontend/src/hooks/useSSE.ts
@@ -3,6 +3,11 @@
  *
  * Creates an EventSource when `url` is non-null; closes on cleanup or when
  * the stream ends. No auto-reconnect — our SSE streams are finite.
+ *
+ * Features:
+ * - Automatic timeout detection (60s without messages triggers error)
+ * - Heartbeat support (server sends ": heartbeat" comments to keep alive)
+ * - Clean error handling and connection cleanup
  */
 
 import { useEffect, useRef } from "react";
@@ -12,11 +17,13 @@ export interface UseSSEOptions {
   url: string | null;
   /** Called for every `data:` line (already JSON-parsed). */
   onMessage: (data: unknown) => void;
-  /** Called on EventSource errors. */
+  /** Called on EventSource errors or timeout. */
   onError?: (error: Event) => void;
+  /** Timeout in milliseconds (default: 60000 = 60s). Set to 0 to disable. */
+  timeout?: number;
 }
 
-export function useSSE({ url, onMessage, onError }: UseSSEOptions): void {
+export function useSSE({ url, onMessage, onError, timeout = 60000 }: UseSSEOptions): void {
   // Store latest callbacks in refs so we never re-open a connection just
   // because the caller created a new closure.
   const onMessageRef = useRef(onMessage);
@@ -31,17 +38,38 @@ export function useSSE({ url, onMessage, onError }: UseSSEOptions): void {
     if (!url) return;
 
     const es = new EventSource(url);
+    let timeoutId: ReturnType<typeof setTimeout> | null = null;
+
+    // Start timeout timer if enabled
+    const resetTimeout = () => {
+      if (timeout > 0) {
+        if (timeoutId) clearTimeout(timeoutId);
+        timeoutId = setTimeout(() => {
+          // No messages received for timeout duration — connection likely dead
+          const timeoutError = new Event('timeout');
+          onErrorRef.current?.(timeoutError);
+          es.close();
+        }, timeout);
+      }
+    };
+
+    resetTimeout(); // Initial timeout
 
     es.onmessage = (event: MessageEvent) => {
+      // Reset timeout on any message (including heartbeats)
+      resetTimeout();
+
       try {
         const data: unknown = JSON.parse(event.data as string);
         onMessageRef.current(data);
       } catch {
-        // Ignore non-JSON messages (e.g., keep-alive pings)
+        // Ignore non-JSON messages (e.g., ": heartbeat" comment lines)
+        // These still reset the timeout above, which is their purpose
       }
     };
 
     es.onerror = (event: Event) => {
+      if (timeoutId) clearTimeout(timeoutId);
       onErrorRef.current?.(event);
       // The server closes the stream on terminal events, which fires an error
       // event with readyState CLOSED. We just close our side too.
@@ -49,7 +77,8 @@ export function useSSE({ url, onMessage, onError }: UseSSEOptions): void {
     };
 
     return () => {
+      if (timeoutId) clearTimeout(timeoutId);
       es.close();
     };
-  }, [url]);
+  }, [url, timeout]);
 }

From da5eabbca46127909b1ff9c12efebc07e6627283 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:16:22 -0700
Subject: [PATCH 151/173] Frontend: Add Settings for performance tuning

---
 .../settings/PerformanceSection.tsx           | 262 ++++++++++++++++++
 1 file changed, 262 insertions(+)
 create mode 100644 frontend/src/components/settings/PerformanceSection.tsx

diff --git a/frontend/src/components/settings/PerformanceSection.tsx b/frontend/src/components/settings/PerformanceSection.tsx
new file mode 100644
index 0000000..9bb2543
--- /dev/null
+++ b/frontend/src/components/settings/PerformanceSection.tsx
@@ -0,0 +1,262 @@
+/**
+ * Performance settings section for batch processing configuration.
+ *
+ * Allows users to configure:
+ * - Skip MCAP validation (fast filename-only parsing)
+ * - Batch size for large uploads
+ * - Auto-tune workers based on CPU
+ * - Max worker count
+ *
+ * Settings auto-save after changes (debounced for continuous inputs like sliders).
+ */
+
+import { useCallback, useEffect, useRef, useState } from "react";
+import { useAppStore } from "../../stores/appStore.ts";
+import type { BatchProcessingSettings, ValueSource } from "../../types/api.ts";
+import { CheckIcon, InfoIcon, SpinnerIcon } from "../../utils/icons.tsx";
+
+function SectionSourceNote({ source }: { source?: ValueSource }) {
+  if (!source || source.source === "builtin") return null;
+
+  if (source.source === "settings_file" || source.source === "default_file") {
+    const filename = source.path?.split("/").pop() ?? source.path ?? "";
+    const label =
+      source.source === "default_file"
+        ? `Default values — ${filename}`
+        : `Saved in ${filename}`;
+    return (
+      <p className="text-xs text-gray-400" title={source.path}>
+        {label}
+      </p>
+    );
+  }
+
+  return null; // batch_processing has no env override support
+}
+
+function getDefaultSettings(): BatchProcessingSettings {
+  return {
+    enabled: true,
+    batch_size: 100,
+    auto_tune_workers: true,
+    max_workers: 4,
+    target_cpu_percent: 70.0,
+    skip_mcap_validation: false,
+    use_database_for_large_jobs: true,
+    large_job_threshold: 1000,
+  };
+}
+
+type SaveStatus = "idle" | "saving" | "saved" | "error";
+
+export default function PerformanceSection() {
+  const { settings: appSettings, updateSettings } = useAppStore();
+  const batchSource = appSettings?.value_sources?.["batch_processing"];
+
+  const [settings, setSettings] = useState<BatchProcessingSettings>(
+    appSettings?.batch_processing ?? getDefaultSettings(),
+  );
+  const [saveStatus, setSaveStatus] = useState<SaveStatus>("idle");
+
+  // Track whether a change originated from the user (vs. store sync).
+  const userChangedRef = useRef(false);
+  const debounceRef = useRef<ReturnType<typeof setTimeout> | null>(null);
+  const savedTimerRef = useRef<ReturnType<typeof setTimeout> | null>(null);
+
+  // Re-sync from the store when settings are loaded externally (e.g. page
+  // navigation reload), but only when there is no pending user change.
+  useEffect(() => {
+    if (appSettings?.batch_processing && !userChangedRef.current) {
+      setSettings(appSettings.batch_processing);
+    }
+  }, [appSettings]);
+
+  // Cleanup timers on unmount.
+  useEffect(() => {
+    return () => {
+      if (debounceRef.current !== null) clearTimeout(debounceRef.current);
+      if (savedTimerRef.current !== null) clearTimeout(savedTimerRef.current);
+    };
+  }, []);
+
+  const save = useCallback(
+    async (toSave: BatchProcessingSettings) => {
+      setSaveStatus("saving");
+      try {
+        await updateSettings({ batch_processing: toSave });
+        userChangedRef.current = false;
+        setSaveStatus("saved");
+        // Clear "saved" indicator after 2 seconds.
+        savedTimerRef.current = setTimeout(() => setSaveStatus("idle"), 2000);
+      } catch {
+        setSaveStatus("error");
+      }
+    },
+    [updateSettings],
+  );
+
+  function handleChange(field: keyof BatchProcessingSettings, value: unknown) {
+    const next = { ...settings, [field]: value };
+    setSettings(next);
+    userChangedRef.current = true;
+
+    // Debounce the save so continuous inputs (sliders) don't fire on every tick.
+    if (debounceRef.current !== null) clearTimeout(debounceRef.current);
+    if (savedTimerRef.current !== null) clearTimeout(savedTimerRef.current);
+    debounceRef.current = setTimeout(() => save(next), 600);
+  }
+
+  async function handleReset() {
+    const defaults = getDefaultSettings();
+    setSettings(defaults);
+    userChangedRef.current = true;
+    if (debounceRef.current !== null) clearTimeout(debounceRef.current);
+    if (savedTimerRef.current !== null) clearTimeout(savedTimerRef.current);
+    await save(defaults);
+  }
+
+  return (
+    <div className="bg-white rounded-lg shadow p-6">
+      <div className="flex items-baseline justify-between mb-4">
+        <div className="flex items-center gap-3">
+          <h3 className="text-lg font-semibold text-nlr-text">Performance</h3>
+          {saveStatus === "saving" && (
+            <span className="flex items-center gap-1 text-xs text-gray-400">
+              <SpinnerIcon className="w-3 h-3 animate-spin" />
+              Saving...
+            </span>
+          )}
+          {saveStatus === "saved" && (
+            <span className="flex items-center gap-1 text-xs text-green-600">
+              <CheckIcon className="w-3 h-3" />
+              Saved
+            </span>
+          )}
+          {saveStatus === "error" && (
+            <span className="text-xs text-red-600">Save failed</span>
+          )}
+        </div>
+        <SectionSourceNote source={batchSource} />
+      </div>
+
+      <div className="space-y-6">
+        {/* Skip MCAP Validation */}
+        <div className="flex items-start gap-3">
+          <input
+            type="checkbox"
+            id="skip_mcap_validation"
+            checked={settings.skip_mcap_validation}
+            onChange={(e) => handleChange("skip_mcap_validation", e.target.checked)}
+            className="mt-1 h-4 w-4 text-nlr-blue border-gray-300 rounded focus:ring-nlr-blue"
+          />
+          <div className="flex-1">
+            <label htmlFor="skip_mcap_validation" className="text-sm font-medium text-gray-700 cursor-pointer">
+              Skip MCAP Validation (Fast Mode)
+            </label>
+            <p className="text-xs text-gray-500 mt-1">
+              Extract timestamps from filenames only (3000x faster). Use when filenames are correctly formatted.
+            </p>
+          </div>
+        </div>
+
+        {/* Batch Size */}
+        <div>
+          <label htmlFor="batch_size" className="block text-sm font-medium text-gray-700 mb-2">
+            Batch Size: <span className="font-semibold">{settings.batch_size}</span>
+          </label>
+          <input
+            type="range"
+            id="batch_size"
+            min="50"
+            max="500"
+            step="50"
+            value={settings.batch_size}
+            onChange={(e) => handleChange("batch_size", Number.parseInt(e.target.value))}
+            className="w-full h-2 bg-gray-200 rounded-lg appearance-none cursor-pointer accent-nlr-blue"
+          />
+          <p className="text-xs text-gray-500 mt-1">
+            Number of files processed per batch (50-500). Lower values reduce memory usage.
+          </p>
+        </div>
+
+        {/* Auto-tune Workers */}
+        <div className="flex items-start gap-3">
+          <input
+            type="checkbox"
+            id="auto_tune_workers"
+            checked={settings.auto_tune_workers}
+            onChange={(e) => handleChange("auto_tune_workers", e.target.checked)}
+            className="mt-1 h-4 w-4 text-nlr-blue border-gray-300 rounded focus:ring-nlr-blue"
+          />
+          <div className="flex-1">
+            <label htmlFor="auto_tune_workers" className="text-sm font-medium text-gray-700 cursor-pointer">
+              Auto-Tune Workers
+            </label>
+            <p className="text-xs text-gray-500 mt-1">
+              Automatically adjust worker count based on CPU/memory utilization. Recommended for large jobs.
+            </p>
+          </div>
+        </div>
+
+        {/* Max Workers */}
+        <div>
+          <label htmlFor="max_workers" className="block text-sm font-medium text-gray-700 mb-2">
+            Max Workers
+          </label>
+          <input
+            type="number"
+            id="max_workers"
+            min="2"
+            max="16"
+            value={settings.max_workers}
+            onChange={(e) => handleChange("max_workers", Number.parseInt(e.target.value))}
+            className="w-32 px-3 py-2 text-sm border border-gray-300 rounded-md focus:outline-none focus:ring-2 focus:ring-nlr-blue"
+          />
+          <p className="text-xs text-gray-500 mt-1">
+            Maximum concurrent workers (2-16). Higher values increase throughput but use more resources.
+          </p>
+        </div>
+
+        {/* Large Job Threshold */}
+        <div>
+          <label htmlFor="large_job_threshold" className="block text-sm font-medium text-gray-700 mb-2">
+            Large Job Threshold
+          </label>
+          <input
+            type="number"
+            id="large_job_threshold"
+            min="100"
+            max="10000"
+            step="100"
+            value={settings.large_job_threshold}
+            onChange={(e) => handleChange("large_job_threshold", Number.parseInt(e.target.value))}
+            className="w-32 px-3 py-2 text-sm border border-gray-300 rounded-md focus:outline-none focus:ring-2 focus:ring-nlr-blue"
+          />
+          <p className="text-xs text-gray-500 mt-1">
+            Jobs with more files than this threshold use batch processing and database storage.
+          </p>
+        </div>
+
+        {/* Info banner */}
+        <div className="flex items-start gap-2 p-3 bg-blue-50 rounded-lg border border-blue-200 text-sm text-blue-700">
+          <InfoIcon className="w-4 h-4 flex-shrink-0 mt-0.5" />
+          <div>
+            Batch processing optimizes memory usage and performance for large uploads (1000+ files).
+            Results are stored in a database and retrieved on demand.
+          </div>
+        </div>
+
+        {/* Reset button */}
+        <div className="flex items-center gap-3 pt-2">
+          <button
+            type="button"
+            onClick={handleReset}
+            className="px-4 py-2 text-sm font-medium text-gray-700 border border-gray-300 rounded-md hover:bg-gray-50 transition-colors"
+          >
+            Reset to Defaults
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+}

From 42e938d570f0a1af94b7018a704bc7dd969e595a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:16:54 -0700
Subject: [PATCH 152/173] Frontend: Add list of active files

---
 .../src/components/upload/ActiveFilesList.tsx | 104 ++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 frontend/src/components/upload/ActiveFilesList.tsx

diff --git a/frontend/src/components/upload/ActiveFilesList.tsx b/frontend/src/components/upload/ActiveFilesList.tsx
new file mode 100644
index 0000000..9d92eb5
--- /dev/null
+++ b/frontend/src/components/upload/ActiveFilesList.tsx
@@ -0,0 +1,104 @@
+/**
+ * Compact list showing only files currently being uploaded.
+ *
+ * Displays up to 8 active files with:
+ * - Filename
+ * - File size
+ * - Upload progress bar
+ * - Status indicator
+ *
+ * Used during upload phase to show real-time activity without
+ * overwhelming the UI with thousands of rows.
+ */
+
+import type { FileUploadState } from "../../types/api.ts";
+import { formatBytes } from "../../utils/format/bytes.ts";
+import ProgressBar from "../common/ProgressBar.tsx";
+import Spinner from "../common/Spinner.tsx";
+import { CheckIcon, XIcon, WarningIcon } from "../../utils/icons.tsx";
+
+interface ActiveFilesListProps {
+  /** Currently active files (max 8) */
+  files: FileUploadState[];
+}
+
+export default function ActiveFilesList({ files }: ActiveFilesListProps) {
+  if (files.length === 0) {
+    return (
+      <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-8 text-center">
+        <p className="text-gray-500 text-sm">No files currently uploading</p>
+      </div>
+    );
+  }
+
+  return (
+    <div className="space-y-3">
+      <div className="flex items-center justify-between">
+        <h3 className="text-sm font-semibold text-gray-700">Currently Uploading</h3>
+        <span className="text-xs text-gray-500">{files.length} active</span>
+      </div>
+
+      <div className="space-y-2">
+        {files.map((file) => (
+          <ActiveFileCard key={file.local_path} file={file} />
+        ))}
+      </div>
+    </div>
+  );
+}
+
+function ActiveFileCard({ file }: { file: FileUploadState }) {
+  const statusIcon = getStatusIcon(file.status);
+
+  return (
+    <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-3">
+      <div className="flex items-start justify-between gap-3 mb-2">
+        <div className="flex-1 min-w-0">
+          <div className="flex items-center gap-2">
+            <p className="text-sm font-medium text-gray-900 truncate">{file.filename}</p>
+            {statusIcon}
+          </div>
+          <p className="text-xs text-gray-500 mt-0.5">
+            {formatBytes(file.file_size)}
+            {file.status === "uploading" && file.bytes_uploaded > 0 && (
+              <span className="ml-2">
+                {formatBytes(file.bytes_uploaded)} uploaded
+              </span>
+            )}
+          </p>
+        </div>
+      </div>
+
+      {/* Progress bar for uploading files */}
+      {file.status === "uploading" && (
+        <div className="mt-2">
+          <ProgressBar percent={file.progress_percent} color="bg-nlr-blue" />
+        </div>
+      )}
+
+      {/* Error message for failed files */}
+      {file.status === "failed" && file.error_message && (
+        <div className="mt-2 text-xs text-red-600 bg-red-50 rounded px-2 py-1">
+          {file.error_message}
+        </div>
+      )}
+    </div>
+  );
+}
+
+function getStatusIcon(status: string) {
+  switch (status) {
+    case "uploading":
+      return <Spinner size="sm" />;
+    case "completed":
+      return <CheckIcon className="w-4 h-4 text-green-600 flex-shrink-0" />;
+    case "failed":
+      return <XIcon className="w-4 h-4 text-red-600 flex-shrink-0" />;
+    case "skipped":
+      return <WarningIcon className="w-4 h-4 text-yellow-600 flex-shrink-0" />;
+    case "analyzing":
+      return <Spinner size="sm" />;
+    default:
+      return null;
+  }
+}

From c0e75bc2562100a02d2a836ef5b2809bd2ee263a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:17:48 -0700
Subject: [PATCH 153/173] Frontend: Add new batch progress component

---
 .../src/components/upload/BatchProgress.tsx   | 131 ++++++++++++++++++
 1 file changed, 131 insertions(+)
 create mode 100644 frontend/src/components/upload/BatchProgress.tsx

diff --git a/frontend/src/components/upload/BatchProgress.tsx b/frontend/src/components/upload/BatchProgress.tsx
new file mode 100644
index 0000000..89aeeb1
--- /dev/null
+++ b/frontend/src/components/upload/BatchProgress.tsx
@@ -0,0 +1,131 @@
+/**
+ * Batch progress indicator for large upload jobs.
+ *
+ * Shows:
+ * - Current batch number (e.g., "Batch 5/200")
+ * - Progress bar for current batch
+ * - Cumulative job statistics
+ * - Active files being processed (max 8)
+ *
+ * Used during upload phase for jobs processed in batches.
+ */
+
+import type { BatchState } from "../../types/api.ts";
+import ProgressBar from "../common/ProgressBar.tsx";
+import Spinner from "../common/Spinner.tsx";
+import { InfoIcon } from "../../utils/icons.tsx";
+
+interface BatchProgressProps {
+  /** Current batch state */
+  batchState: BatchState | null;
+
+  /** Overall job progress (0-100) */
+  jobProgressPercent: number;
+
+  /** Total files completed across all batches */
+  jobFilesCompleted: number;
+
+  /** Total files in entire job */
+  jobFilesTotal: number;
+
+  /** Total files uploaded successfully across all batches */
+  jobFilesUploaded: number;
+
+  /** Total files failed across all batches */
+  jobFilesFailed: number;
+
+  /** Whether the job is actively running */
+  isRunning: boolean;
+}
+
+export default function BatchProgress({
+  batchState,
+  jobProgressPercent,
+  jobFilesCompleted,
+  jobFilesTotal,
+  jobFilesUploaded,
+  jobFilesFailed,
+  isRunning,
+}: BatchProgressProps) {
+  if (!batchState) {
+    return null;
+  }
+
+  const batchProgressPercent = batchState.files_in_batch > 0
+    ? (batchState.files_processed / batchState.files_in_batch) * 100
+    : 0;
+
+  const currentBatch = batchState.batch_id + 1; // 0-indexed to 1-indexed
+  const totalBatches = batchState.total_batches;
+
+  return (
+    <div className="space-y-4 animate-in fade-in duration-200">
+      {/* Batch indicator */}
+      <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-4">
+        <div className="flex items-center justify-between mb-3">
+          <div className="flex items-center gap-2">
+            <h3 className="text-sm font-semibold text-gray-900">
+              Batch {currentBatch} of {totalBatches}
+            </h3>
+            {isRunning && batchState.status === "processing" && <Spinner size="sm" />}
+          </div>
+          <div className="text-xs text-gray-500">
+            {batchState.files_in_batch} files in this batch
+          </div>
+        </div>
+
+        {/* Batch progress */}
+        <ProgressBar
+          percent={batchProgressPercent}
+          label={`${batchState.files_processed} / ${batchState.files_in_batch} files processed`}
+          color="bg-nlr-blue"
+        />
+
+        {/* Batch stats */}
+        <div className="flex items-center justify-between mt-2 text-xs text-gray-500">
+          <span>
+            Uploaded: {batchState.files_uploaded} | Failed: {batchState.files_failed}
+          </span>
+          {batchState.status === "completed" && batchState.duration_seconds && (
+            <span>{batchState.duration_seconds.toFixed(1)}s</span>
+          )}
+        </div>
+      </div>
+
+      {/* Overall job progress */}
+      <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-4">
+        <div className="flex items-center justify-between mb-3">
+          <h3 className="text-sm font-semibold text-gray-900">Overall Progress</h3>
+        </div>
+
+        <ProgressBar
+          percent={jobProgressPercent}
+          label={`${jobFilesCompleted} / ${jobFilesTotal} total files`}
+          color="bg-green-600"
+        />
+
+        {/* Job stats */}
+        <div className="flex items-center justify-between mt-2 text-xs text-gray-500">
+          <span>
+            Uploaded: {jobFilesUploaded} | Failed: {jobFilesFailed}
+          </span>
+          <span>
+            {totalBatches - currentBatch} batch{totalBatches - currentBatch !== 1 ? "es" : ""} remaining
+          </span>
+        </div>
+      </div>
+
+      {/* Info banner */}
+      {totalBatches > 10 && (
+        <div className="flex items-start gap-2 p-3 bg-blue-50 rounded-lg border border-blue-200 text-sm text-blue-700">
+          <InfoIcon className="w-4 h-4 flex-shrink-0 mt-0.5" />
+          <div>
+            <strong>Large job detected:</strong> Files are being processed in batches
+            to optimize memory usage and performance. Full results will be available
+            after completion.
+          </div>
+        </div>
+      )}
+    </div>
+  );
+}

From 9d910cc4da558fddfefec49b199145cbf70b99b8 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:18:04 -0700
Subject: [PATCH 154/173] Frontend: Add full screen cancel modal that locks
 screen

---
 .../src/components/upload/CancelScanModal.tsx | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 frontend/src/components/upload/CancelScanModal.tsx

diff --git a/frontend/src/components/upload/CancelScanModal.tsx b/frontend/src/components/upload/CancelScanModal.tsx
new file mode 100644
index 0000000..5545ef6
--- /dev/null
+++ b/frontend/src/components/upload/CancelScanModal.tsx
@@ -0,0 +1,63 @@
+/**
+ * Confirmation modal shown when the user tries to cancel a folder scan.
+ */
+
+import Modal from "../common/Modal.tsx";
+import { WarningIcon } from "../../utils/icons.tsx";
+
+interface CancelScanModalProps {
+  isOpen: boolean;
+  onClose: () => void;
+  onConfirm: () => void;
+  foldersScanned: number;
+  filesFound: number;
+}
+
+export default function CancelScanModal({
+  isOpen,
+  onClose,
+  onConfirm,
+  foldersScanned,
+  filesFound,
+}: CancelScanModalProps) {
+  return (
+    <Modal
+      isOpen={isOpen}
+      onClose={onClose}
+      title="Cancel Folder Scan?"
+      footer={
+        <div className="flex gap-3">
+          <button
+            type="button"
+            onClick={onClose}
+            className="px-4 py-2 text-sm font-medium text-gray-600 border border-gray-300 rounded hover:bg-gray-50"
+          >
+            Keep Scanning
+          </button>
+          <button
+            type="button"
+            onClick={onConfirm}
+            className="px-4 py-2 text-sm font-medium rounded transition-colors bg-red-600 text-white hover:bg-red-700"
+          >
+            Cancel Scan
+          </button>
+        </div>
+      }
+    >
+      <div className="space-y-3">
+        <div className="flex items-start gap-3 p-3 bg-amber-50 rounded-lg border border-amber-200">
+          <WarningIcon className="w-5 h-5 text-amber-600 flex-shrink-0 mt-0.5" />
+          <div className="text-sm text-amber-800">
+            <p>
+              Scanning has found <strong>{filesFound}</strong> file{filesFound !== 1 ? "s" : ""} in{" "}
+              <strong>{foldersScanned}</strong> folder{foldersScanned !== 1 ? "s" : ""} so far.
+            </p>
+            <p className="mt-2 text-amber-700">
+              Cancelling will stop the scan and you'll need to start over if you want to continue.
+            </p>
+          </div>
+        </div>
+      </div>
+    </Modal>
+  );
+}

From 3426624c4036bafaca179aa00d32e00f9493292a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:18:31 -0700
Subject: [PATCH 155/173] Frontend: Add scan progress modal

---
 .../components/upload/ScanProgressModal.tsx   | 169 ++++++++++++++++++
 1 file changed, 169 insertions(+)
 create mode 100644 frontend/src/components/upload/ScanProgressModal.tsx

diff --git a/frontend/src/components/upload/ScanProgressModal.tsx b/frontend/src/components/upload/ScanProgressModal.tsx
new file mode 100644
index 0000000..f0073c0
--- /dev/null
+++ b/frontend/src/components/upload/ScanProgressModal.tsx
@@ -0,0 +1,169 @@
+/**
+ * Modal overlay that shows folder scan progress.
+ *
+ * Displayed when scanning a folder with many files to give users
+ * clear feedback about what's happening and how long it might take.
+ */
+
+import { useEffect, useRef, useState } from "react";
+import { formatBytes } from "../../utils/format/bytes.ts";
+import ProgressBar from "../common/ProgressBar.tsx";
+import Spinner from "../common/Spinner.tsx";
+import { XIcon } from "../../utils/icons.tsx";
+import CancelScanModal from "./CancelScanModal.tsx";
+
+interface ScanProgressModalProps {
+  isOpen: boolean;
+  foldersScanned: number;
+  foldersTotal: number;
+  totalFiles: number;
+  totalSize: number;
+  folderPath: string;
+  onCancel: () => void;
+}
+
+export default function ScanProgressModal({
+  isOpen,
+  foldersScanned,
+  foldersTotal,
+  totalFiles,
+  totalSize,
+  folderPath,
+  onCancel,
+}: ScanProgressModalProps) {
+  const backdropRef = useRef<HTMLDivElement>(null);
+  const [showCancelConfirm, setShowCancelConfirm] = useState(false);
+
+  // Calculate scan progress percentage
+  const progressPercent = foldersTotal > 0 ? Math.round((foldersScanned / foldersTotal) * 100) : 0;
+
+  const handleCancelClick = () => {
+    setShowCancelConfirm(true);
+  };
+
+  const handleConfirmCancel = () => {
+    setShowCancelConfirm(false);
+    onCancel();
+  };
+
+  // Handle Escape key - show confirmation
+  useEffect(() => {
+    if (!isOpen) return;
+
+    function handleKeyDown(e: KeyboardEvent) {
+      if (e.key === "Escape") handleCancelClick();
+    }
+
+    document.addEventListener("keydown", handleKeyDown);
+    return () => document.removeEventListener("keydown", handleKeyDown);
+  }, [isOpen]);
+
+  if (!isOpen) return null;
+
+  function handleBackdropClick(e: React.MouseEvent) {
+    if (e.target === backdropRef.current) handleCancelClick();
+  }
+
+  return (
+    <>
+    <div
+      ref={backdropRef}
+      className="fixed inset-0 bg-black/50 z-50 flex items-center justify-center animate-[fadeIn_0.15s_ease-out]"
+      onClick={handleBackdropClick}
+    >
+      <div className="bg-white rounded-lg shadow-xl max-w-2xl w-full mx-4 overflow-hidden">
+        <div className="p-6">
+        {/* Header */}
+        <div className="flex items-start justify-between mb-6">
+          <div className="flex items-center gap-3">
+            <Spinner size="md" />
+            <div>
+              <h3 className="text-lg font-semibold text-gray-900">Scanning Folder</h3>
+              <p className="text-sm text-gray-500 mt-1">
+                Searching for MCAP files and checking upload status...
+              </p>
+            </div>
+          </div>
+          <button
+            type="button"
+            onClick={handleCancelClick}
+            className="text-gray-400 hover:text-gray-600 transition-colors"
+            title="Cancel scan"
+          >
+            <XIcon className="w-5 h-5" />
+          </button>
+        </div>
+
+        {/* Folder path */}
+        <div className="mb-6 p-3 bg-gray-50 rounded-lg">
+          <p className="text-xs text-gray-500 uppercase tracking-wide mb-1">Scanning</p>
+          <p className="text-sm text-gray-900 font-mono truncate" title={folderPath}>
+            {folderPath}
+          </p>
+        </div>
+
+        {/* Progress bar */}
+        {foldersTotal > 0 && (
+          <div className="mb-6">
+            <div className="flex items-center justify-between mb-2">
+              <span className="text-sm font-medium text-gray-700">Progress</span>
+              <span className="text-sm font-bold text-nlr-blue">{progressPercent}%</span>
+            </div>
+            <ProgressBar percent={progressPercent} color="bg-nlr-blue" />
+            <p className="text-xs text-gray-500 mt-2">
+              {foldersScanned} of {foldersTotal} folders scanned
+            </p>
+          </div>
+        )}
+
+        {/* Progress stats */}
+        <div className="grid grid-cols-3 gap-4 mb-6">
+          <StatCard value={foldersScanned} label="Folders Scanned" />
+          <StatCard value={totalFiles} label="Files Found" />
+          <StatCard value={formatBytes(totalSize)} label="Total Size" />
+        </div>
+
+        {/* Info message */}
+        <div className="bg-blue-50 border border-blue-200 rounded-lg p-4 mb-6">
+          <p className="text-sm text-blue-800">
+            <strong>Note:</strong> Scanning large folders with thousands of files may take a few
+            minutes. Each file is checked against the upload cache to determine if it's already been
+            uploaded to S3.
+          </p>
+        </div>
+
+        {/* Cancel button */}
+        <div className="flex justify-end">
+          <button
+            type="button"
+            onClick={handleCancelClick}
+            className="px-4 py-2 text-sm font-medium text-gray-700 bg-white border border-gray-300 rounded-md hover:bg-gray-50 transition-colors"
+          >
+            Cancel Scan
+          </button>
+        </div>
+        </div>
+      </div>
+    </div>
+    {/* Cancel confirmation modal */}
+    <CancelScanModal
+      isOpen={showCancelConfirm}
+      onClose={() => setShowCancelConfirm(false)}
+      onConfirm={handleConfirmCancel}
+      foldersScanned={foldersScanned}
+      filesFound={totalFiles}
+    />
+  </>
+  );
+}
+
+function StatCard({ value, label }: { value: number | string; label: string }) {
+  return (
+    <div className="bg-white border border-gray-200 rounded-lg p-3 text-center">
+      <div className="text-2xl font-bold text-nlr-blue">
+        {typeof value === "number" ? value.toLocaleString() : value}
+      </div>
+      <div className="text-xs text-gray-500 mt-1">{label}</div>
+    </div>
+  );
+}

From 1562209413d998b84d086ed59be0b987f1670867 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:19:26 -0700
Subject: [PATCH 156/173] Frontend: Add data source provenance to file derived
 settings

---
 .../src/components/settings/SettingsForm.tsx  | 141 +++++++++++-------
 1 file changed, 84 insertions(+), 57 deletions(-)

diff --git a/frontend/src/components/settings/SettingsForm.tsx b/frontend/src/components/settings/SettingsForm.tsx
index 5f74fc2..9817cc8 100644
--- a/frontend/src/components/settings/SettingsForm.tsx
+++ b/frontend/src/components/settings/SettingsForm.tsx
@@ -1,10 +1,41 @@
 import { useEffect, useState } from "react";
 import { apiGet, apiPost } from "../../api/client.ts";
 import { useAppStore } from "../../stores/appStore.ts";
-import type { AppSettings, ConnectionTestResult } from "../../types/api.ts";
+import type { AppSettings, ConnectionTestResult, ValueSource } from "../../types/api.ts";
+import { LockIcon } from "../../utils/icons.tsx";
 
 const AWS_REGIONS = ["us-east-1", "us-east-2", "us-west-1", "us-west-2"];
 
+/** Shows where a setting value comes from and locks the field if it is env-overridden. */
+function SourceBadge({ source }: { source?: ValueSource }) {
+  if (!source) return null;
+
+  if (source.source === "env") {
+    return (
+      <span className="flex items-center gap-1 mt-1 text-xs text-amber-600 font-medium">
+        <LockIcon className="w-3 h-3 flex-shrink-0" />
+        Locked — set by environment variable{" "}
+        <code className="font-mono">{source.env_var}</code>
+      </span>
+    );
+  }
+
+  if (source.source === "settings_file" || source.source === "default_file") {
+    const filename = source.path?.split("/").pop() ?? source.path ?? "";
+    const label =
+      source.source === "default_file"
+        ? `Default — ${filename}`
+        : `Saved in ${filename}`;
+    return (
+      <span className="mt-1 text-xs text-gray-400" title={source.path}>
+        {label}
+      </span>
+    );
+  }
+
+  return <span className="mt-1 text-xs text-gray-400">Built-in default</span>;
+}
+
 export default function SettingsForm() {
   const { settings, updateSettings } = useAppStore();
 
@@ -16,9 +47,7 @@ export default function SettingsForm() {
 
   // Connection test state
   const [testing, setTesting] = useState(false);
-  const [testResult, setTestResult] = useState<ConnectionTestResult | null>(
-    null,
-  );
+  const [testResult, setTestResult] = useState<ConnectionTestResult | null>(null);
 
   // Load profiles on mount
   useEffect(() => {
@@ -40,13 +69,17 @@ export default function SettingsForm() {
         display_name: settings.display_name,
         log_directory: settings.log_directory,
       });
-      // Check if the current region is not in our standard list
       setCustomRegion(!AWS_REGIONS.includes(settings.aws_region));
       setIsDirty(false);
     }
   }, [settings]);
 
+  function isLocked(field: keyof AppSettings): boolean {
+    return settings?.value_sources?.[field]?.source === "env";
+  }
+
   function handleChange(field: keyof AppSettings, value: string) {
+    if (isLocked(field)) return;
     setFormValues((prev) => ({ ...prev, [field]: value }));
     setIsDirty(true);
     setTestResult(null);
@@ -66,14 +99,11 @@ export default function SettingsForm() {
     setTesting(true);
     setTestResult(null);
     try {
-      const result = await apiPost<ConnectionTestResult>(
-        "/api/settings/validate",
-        {
-          aws_profile: formValues.aws_profile,
-          aws_region: formValues.aws_region,
-          s3_bucket: formValues.s3_bucket,
-        },
-      );
+      const result = await apiPost<ConnectionTestResult>("/api/settings/validate", {
+        aws_profile: formValues.aws_profile,
+        aws_region: formValues.aws_region,
+        s3_bucket: formValues.s3_bucket,
+      });
       setTestResult(result);
     } catch {
       setTestResult({ success: false, error: "Connection test failed" });
@@ -85,55 +115,54 @@ export default function SettingsForm() {
   async function handleSave() {
     setSaving(true);
     try {
-      await updateSettings(formValues);
+      // Filter out env-overridden keys — they can't be changed anyway
+      const vsrc = settings?.value_sources ?? {};
+      const toSave = Object.fromEntries(
+        Object.entries(formValues).filter(([k]) => vsrc[k]?.source !== "env"),
+      );
+      await updateSettings(toSave);
       setIsDirty(false);
     } finally {
       setSaving(false);
     }
   }
 
+  const inputBase =
+    "w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none";
+  const inputLocked = "bg-gray-50 text-gray-500 cursor-not-allowed";
+
   return (
     <div className="bg-white rounded-lg shadow p-6">
-      <h3 className="text-lg font-semibold text-nlr-text mb-4">
-        AWS Configuration
-      </h3>
+      <h3 className="text-lg font-semibold text-nlr-text mb-4">AWS Configuration</h3>
 
       <div className="space-y-4">
         {/* AWS Profile */}
         <div>
-          <label
-            htmlFor="aws_profile"
-            className="block text-sm font-medium text-gray-700 mb-1"
-          >
+          <label htmlFor="aws_profile" className="block text-sm font-medium text-gray-700 mb-1">
             AWS Profile
           </label>
           <select
             id="aws_profile"
             value={formValues.aws_profile ?? ""}
             onChange={(e) => handleChange("aws_profile", e.target.value)}
-            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+            disabled={isLocked("aws_profile")}
+            className={`${inputBase} ${isLocked("aws_profile") ? inputLocked : ""}`}
           >
             {profiles.map((p) => (
               <option key={p} value={p}>
                 {p}
               </option>
             ))}
-            {/* If current profile is not in profiles list, show it anyway */}
-            {formValues.aws_profile &&
-              !profiles.includes(formValues.aws_profile) && (
-                <option value={formValues.aws_profile}>
-                  {formValues.aws_profile}
-                </option>
-              )}
+            {formValues.aws_profile && !profiles.includes(formValues.aws_profile) && (
+              <option value={formValues.aws_profile}>{formValues.aws_profile}</option>
+            )}
           </select>
+          <SourceBadge source={settings?.value_sources?.["aws_profile"]} />
         </div>
 
         {/* AWS Region */}
         <div>
-          <label
-            htmlFor="aws_region"
-            className="block text-sm font-medium text-gray-700 mb-1"
-          >
+          <label htmlFor="aws_region" className="block text-sm font-medium text-gray-700 mb-1">
             AWS Region
           </label>
           {!customRegion ? (
@@ -141,7 +170,8 @@ export default function SettingsForm() {
               id="aws_region"
               value={formValues.aws_region ?? ""}
               onChange={(e) => handleRegionSelect(e.target.value)}
-              className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+              disabled={isLocked("aws_region")}
+              className={`${inputBase} ${isLocked("aws_region") ? inputLocked : ""}`}
             >
               {AWS_REGIONS.map((r) => (
                 <option key={r} value={r}>
@@ -158,7 +188,8 @@ export default function SettingsForm() {
                 value={formValues.aws_region ?? ""}
                 onChange={(e) => handleChange("aws_region", e.target.value)}
                 placeholder="e.g., eu-north-1"
-                className="flex-1 rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+                disabled={isLocked("aws_region")}
+                className={`flex-1 rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none ${isLocked("aws_region") ? inputLocked : ""}`}
               />
               <button
                 type="button"
@@ -172,14 +203,12 @@ export default function SettingsForm() {
               </button>
             </div>
           )}
+          <SourceBadge source={settings?.value_sources?.["aws_region"]} />
         </div>
 
         {/* S3 Bucket */}
         <div>
-          <label
-            htmlFor="s3_bucket"
-            className="block text-sm font-medium text-gray-700 mb-1"
-          >
+          <label htmlFor="s3_bucket" className="block text-sm font-medium text-gray-700 mb-1">
             S3 Bucket
           </label>
           <input
@@ -188,8 +217,10 @@ export default function SettingsForm() {
             value={formValues.s3_bucket ?? ""}
             onChange={(e) => handleChange("s3_bucket", e.target.value)}
             placeholder="my-bucket-name"
-            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+            disabled={isLocked("s3_bucket")}
+            className={`${inputBase} ${isLocked("s3_bucket") ? inputLocked : ""}`}
           />
+          <SourceBadge source={settings?.value_sources?.["s3_bucket"]} />
         </div>
 
         {/* Default Upload Folder */}
@@ -204,20 +235,17 @@ export default function SettingsForm() {
             id="default_upload_folder"
             type="text"
             value={formValues.default_upload_folder ?? ""}
-            onChange={(e) =>
-              handleChange("default_upload_folder", e.target.value)
-            }
+            onChange={(e) => handleChange("default_upload_folder", e.target.value)}
             placeholder="/path/to/mcap/files"
-            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+            disabled={isLocked("default_upload_folder")}
+            className={`${inputBase} ${isLocked("default_upload_folder") ? inputLocked : ""}`}
           />
+          <SourceBadge source={settings?.value_sources?.["default_upload_folder"]} />
         </div>
 
         {/* Display Name */}
         <div>
-          <label
-            htmlFor="display_name"
-            className="block text-sm font-medium text-gray-700 mb-1"
-          >
+          <label htmlFor="display_name" className="block text-sm font-medium text-gray-700 mb-1">
             Display Name
           </label>
           <input
@@ -226,16 +254,15 @@ export default function SettingsForm() {
             value={formValues.display_name ?? ""}
             onChange={(e) => handleChange("display_name", e.target.value)}
             placeholder="SURF-WEC MODAQ Uploader"
-            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+            disabled={isLocked("display_name")}
+            className={`${inputBase} ${isLocked("display_name") ? inputLocked : ""}`}
           />
+          <SourceBadge source={settings?.value_sources?.["display_name"]} />
         </div>
 
         {/* Log Directory */}
         <div>
-          <label
-            htmlFor="log_directory"
-            className="block text-sm font-medium text-gray-700 mb-1"
-          >
+          <label htmlFor="log_directory" className="block text-sm font-medium text-gray-700 mb-1">
             Log Directory
           </label>
           <input
@@ -244,8 +271,10 @@ export default function SettingsForm() {
             value={formValues.log_directory ?? ""}
             onChange={(e) => handleChange("log_directory", e.target.value)}
             placeholder="logs"
-            className="w-full rounded-md border border-gray-300 px-3 py-2 text-sm focus:border-nlr-blue focus:ring-1 focus:ring-nlr-blue focus:outline-none"
+            disabled={isLocked("log_directory")}
+            className={`${inputBase} ${isLocked("log_directory") ? inputLocked : ""}`}
           />
+          <SourceBadge source={settings?.value_sources?.["log_directory"]} />
         </div>
       </div>
 
@@ -283,9 +312,7 @@ export default function SettingsForm() {
         </button>
 
         {isDirty && (
-          <span className="text-sm text-nlr-yellow font-medium">
-            Unsaved changes
-          </span>
+          <span className="text-sm text-nlr-yellow font-medium">Unsaved changes</span>
         )}
       </div>
     </div>

From e10e0dd3056292eff4d25d60f47db9990f7ec33f Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:19:58 -0700
Subject: [PATCH 157/173] Frontend: Add analyzing progress to file table

---
 frontend/src/components/upload/UnifiedFileTable.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/src/components/upload/UnifiedFileTable.tsx b/frontend/src/components/upload/UnifiedFileTable.tsx
index 86b897e..84ef595 100644
--- a/frontend/src/components/upload/UnifiedFileTable.tsx
+++ b/frontend/src/components/upload/UnifiedFileTable.tsx
@@ -380,7 +380,7 @@ function StatusBadge({
 
   const labels: Record<string, string> = {
     queued: "queued",
-    in_progress: `${Math.round(progressPercent)}%`,
+    in_progress: progressPercent > 0 ? `${Math.round(progressPercent)}%` : "analyzing",
     completed: "uploaded",
     skipped: "skipped",
     failed: "failed",

From a0fee3c0c97b648afbc9f8eefc28d6711dcbeb2a Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:20:29 -0700
Subject: [PATCH 158/173] Frontend: Refactor upload header with more actionable
 KPI

---
 .../src/components/upload/UploadHeader.tsx    | 108 ++++++++++++++----
 1 file changed, 85 insertions(+), 23 deletions(-)

diff --git a/frontend/src/components/upload/UploadHeader.tsx b/frontend/src/components/upload/UploadHeader.tsx
index ab9a9ef..79575c6 100644
--- a/frontend/src/components/upload/UploadHeader.tsx
+++ b/frontend/src/components/upload/UploadHeader.tsx
@@ -22,7 +22,12 @@ interface UploadHeaderProps {
   phase: UploadPhase;
 
   // Review data
-  totals: { totalFiles: number; alreadyUploaded: number; totalSize: number };
+  totals: {
+    toUpload: number;
+    uploadSize: number;
+    alreadyOnS3: number;
+    totalInFolder: number;
+  };
   isScanning: boolean;
   foldersFound: number;
 
@@ -60,7 +65,13 @@ export default function UploadHeader({
   onFilterClick,
 }: UploadHeaderProps) {
   if (phase === "review") {
-    return <ReviewHeader totals={totals} isScanning={isScanning} foldersFound={foldersFound} />;
+    return (
+      <ReviewHeader
+        totals={totals}
+        isScanning={isScanning}
+        foldersFound={foldersFound}
+      />
+    );
   }
 
   if (phase === "uploading") {
@@ -89,25 +100,46 @@ function ReviewHeader({
   isScanning,
   foldersFound,
 }: {
-  totals: { totalFiles: number; alreadyUploaded: number; totalSize: number };
+  totals: {
+    toUpload: number;
+    uploadSize: number;
+    alreadyOnS3: number;
+    totalInFolder: number;
+  };
   isScanning: boolean;
   foldersFound: number;
 }) {
-  const newFiles = totals.totalFiles - totals.alreadyUploaded;
   return (
     <div className="space-y-3 animate-in fade-in duration-200">
       <div className="grid grid-cols-2 sm:grid-cols-4 gap-3">
-        <StatCard value={totals.totalFiles.toLocaleString()} label="Total Files" color="text-nlr-blue" />
-        <StatCard value={formatBytes(totals.totalSize)} label="Total Size" color="text-nlr-blue" />
-        <StatCard value={totals.alreadyUploaded.toLocaleString()} label="Already Uploaded" color="text-yellow-500" />
-        <StatCard value={newFiles.toLocaleString()} label="New Files" color="text-green-600" />
+        <StatCard
+          value={totals.toUpload.toLocaleString()}
+          label="Files to Upload"
+          color="text-green-600"
+        />
+        <StatCard
+          value={formatBytes(totals.uploadSize)}
+          label="Upload Size"
+          color="text-nlr-blue"
+        />
+        <StatCard
+          value={totals.alreadyOnS3.toLocaleString()}
+          label="Already Uploaded"
+          color="text-yellow-500"
+        />
+        <StatCard
+          value={totals.totalInFolder.toLocaleString()}
+          label="In Folder"
+          color="text-gray-500"
+        />
       </div>
 
       {isScanning && (
         <div className="flex items-center gap-3 p-3 bg-blue-50 rounded-lg border border-blue-200">
           <Spinner size="sm" />
           <span className="text-sm text-blue-700">
-            Scanning folders... ({foldersFound} folder{foldersFound !== 1 ? "s" : ""} found so far)
+            Scanning folders... ({foldersFound} folder
+            {foldersFound !== 1 ? "s" : ""} found so far)
           </span>
         </div>
       )}
@@ -144,7 +176,9 @@ function UploadingHeader({
       <div className="bg-white rounded-lg shadow-sm border border-gray-200 p-4">
         <div className="flex items-center justify-between mb-2">
           <h3 className="text-sm font-semibold text-gray-900">
-            {isRunning && filesProcessed < totalFiles ? "Uploading..." : "Upload Complete"}
+            {isRunning && filesProcessed < totalFiles
+              ? "Uploading..."
+              : "Upload Complete"}
           </h3>
           {isRunning && filesProcessed < totalFiles && <Spinner size="sm" />}
         </div>
@@ -204,11 +238,12 @@ function SummaryHeader({
 }) {
   if (!job) return null;
 
-  const headlineColor = job.files_failed > 0
-    ? "text-yellow-600"
-    : job.cancelled
-      ? "text-gray-600"
-      : "text-green-600";
+  const headlineColor =
+    job.files_failed > 0
+      ? "text-yellow-600"
+      : job.cancelled
+        ? "text-gray-600"
+        : "text-green-600";
 
   const headlineText = job.cancelled
     ? "Upload Cancelled"
@@ -230,32 +265,57 @@ function SummaryHeader({
           onClick={() => onFilterClick?.("completed")}
           className="text-left"
         >
-          <StatCard value={job.files_uploaded.toLocaleString()} label="Uploaded" color="text-green-600" />
+          <StatCard
+            value={job.files_uploaded.toLocaleString()}
+            label="Uploaded"
+            color="text-green-600"
+          />
         </button>
         <button
           type="button"
           onClick={() => onFilterClick?.("skipped")}
           className="text-left"
         >
-          <StatCard value={job.files_skipped.toLocaleString()} label="Skipped" color="text-yellow-500" />
+          <StatCard
+            value={job.files_skipped.toLocaleString()}
+            label="Skipped"
+            color="text-yellow-500"
+          />
         </button>
         <button
           type="button"
           onClick={() => onFilterClick?.("failed")}
           className="text-left"
         >
-          <StatCard value={job.files_failed.toLocaleString()} label="Failed" color="text-red-500" />
+          <StatCard
+            value={job.files_failed.toLocaleString()}
+            label="Failed"
+            color="text-red-500"
+          />
         </button>
-        <StatCard value={job.successfully_uploaded_bytes_formatted} label="Data Uploaded" color="text-nlr-blue" />
-        <StatCard value={formatDuration(job.total_upload_duration_seconds)} label="Duration" color="text-nlr-blue" />
-        <StatCard value={formatSpeed(job.average_upload_speed_mbps)} label="Avg Speed" color="text-nlr-blue" />
+        <StatCard
+          value={job.successfully_uploaded_bytes_formatted}
+          label="Data Uploaded"
+          color="text-nlr-blue"
+        />
+        <StatCard
+          value={formatDuration(job.total_upload_duration_seconds)}
+          label="Duration"
+          color="text-nlr-blue"
+        />
+        <StatCard
+          value={formatSpeed(job.average_upload_speed_mbps)}
+          label="Avg Speed"
+          color="text-nlr-blue"
+        />
       </div>
 
       {job.files_failed > 0 && (
         <div className="flex items-center gap-2 p-3 bg-red-50 rounded-lg border border-red-200 text-sm text-red-700">
           <WarningIcon className="w-4 h-4 flex-shrink-0" />
           <span>
-            <strong>{job.files_failed}</strong> file{job.files_failed !== 1 ? "s" : ""} failed to upload.
+            <strong>{job.files_failed}</strong> file
+            {job.files_failed !== 1 ? "s" : ""} failed to upload.
             <button
               type="button"
               onClick={() => onFilterClick?.("failed")}
@@ -293,7 +353,9 @@ function StatusCounterButton({
       onClick={onClick}
       className={`${bgColor} ${borderColor} border rounded-lg p-3 text-center hover:opacity-80 transition-opacity cursor-pointer`}
     >
-      <div className={`text-xl font-bold ${color}`}>{count.toLocaleString()}</div>
+      <div className={`text-xl font-bold ${color}`}>
+        {count.toLocaleString()}
+      </div>
       <div className="text-xs text-gray-500 mt-0.5">{label}</div>
     </button>
   );

From 41862ff9152aa257a861f043b27762a60c0551fc Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:21:48 -0700
Subject: [PATCH 159/173] Frontend: Add batching support to useUploadJob

---
 frontend/src/hooks/useUploadJob.ts | 105 ++++++++++++++++++++++++++++-
 1 file changed, 103 insertions(+), 2 deletions(-)

diff --git a/frontend/src/hooks/useUploadJob.ts b/frontend/src/hooks/useUploadJob.ts
index 381ba59..7a1f667 100644
--- a/frontend/src/hooks/useUploadJob.ts
+++ b/frontend/src/hooks/useUploadJob.ts
@@ -15,7 +15,11 @@ import type {
   AnalysisCompleteEvent,
   AnalysisProgressEvent,
   AutoUploadStartingEvent,
+  BatchCompletedEvent,
+  BatchProgressEvent,
+  BatchStartedEvent,
   FileUploadState,
+  JobCompletedEvent,
   UploadJob,
   UploadJobProgress,
 } from "../types/api.ts";
@@ -56,6 +60,10 @@ type SSEEvent =
   | AnalysisProgressEvent
   | AnalysisCompleteEvent
   | AutoUploadStartingEvent
+  | BatchStartedEvent
+  | BatchProgressEvent
+  | BatchCompletedEvent
+  | JobCompletedEvent
   | UploadJobProgress
   | UploadJob;
 
@@ -86,7 +94,15 @@ export function useUploadJob(options: UseUploadJobOptions = {}): UseUploadJobRes
   const [totalBytesFormatted, setTotalBytesFormatted] = useState("");
   const [isCancelling, setIsCancelling] = useState(false);
 
-  const { setUploadJobId, setCompletedJob } = useUploadStore();
+  const {
+    setUploadJobId,
+    setCompletedJob,
+    setCurrentBatch,
+    setTotalBatches,
+    setBatchState,
+    setIsBatchProcessing,
+    batchState,
+  } = useUploadStore();
 
   // Callback refs — kept in sync with latest options via effect
   const onFileUpdateRef = useRef(options.onFileUpdate);
@@ -147,6 +163,84 @@ export function useUploadJob(options: UseUploadJobOptions = {}): UseUploadJobRes
             // arrive via progress dicts.
             break;
 
+          case "batch_started": {
+            const evt = data as BatchStartedEvent;
+            setCurrentBatch(evt.batch_id);
+            setTotalBatches(evt.total_batches);
+            setIsBatchProcessing(true);
+            setBatchState({
+              batch_id: evt.batch_id,
+              total_batches: evt.total_batches,
+              files_in_batch: evt.files_in_batch,
+              status: "processing",
+              files_processed: 0,
+              files_uploaded: 0,
+              files_failed: 0,
+              bytes_uploaded: 0,
+              started_at: new Date().toISOString(),
+              completed_at: null,
+              duration_seconds: null,
+              error_message: "",
+            });
+            break;
+          }
+
+          case "batch_progress": {
+            const evt = data as BatchProgressEvent;
+            setCurrentBatch(evt.batch_id);
+            // Limit active files to 8 items max
+            setActiveFiles(evt.active_files.slice(0, 8));
+            setFilesProcessed(evt.job_files_completed);
+            setTotalFiles(evt.job_files_total);
+            setProgressPercent(evt.job_progress_percent);
+
+            // Update batch state with current progress
+            if (batchState) {
+              setBatchState({
+                ...batchState,
+                files_processed: evt.batch_files_completed,
+              });
+            }
+
+            // Notify unified table for each active file
+            if (onFileUpdateRef.current) {
+              for (const file of evt.active_files.slice(0, 8)) {
+                onFileUpdateRef.current(file);
+              }
+            }
+            break;
+          }
+
+          case "batch_completed": {
+            const evt = data as BatchCompletedEvent;
+            if (batchState) {
+              setBatchState({
+                ...batchState,
+                status: "completed",
+                files_uploaded: evt.files_uploaded,
+                files_failed: evt.files_failed,
+                completed_at: new Date().toISOString(),
+              });
+            }
+            break;
+          }
+
+          case "job_completed": {
+            // Job completed event - reset batch state
+            setIsRunning(false);
+            setIsCancelling(false);
+            setJobId(null);
+            setIsBatchProcessing(false);
+            setCurrentBatch(null);
+            setTotalBatches(null);
+            setBatchState(null);
+
+            // For large jobs, fetch paginated results instead of receiving all files
+            // The full file list would be too large for SSE
+            // Client should call /api/upload/results/<job_id> for pagination
+            break;
+          }
+
           default:
             break;
         }
@@ -213,7 +307,14 @@ export function useUploadJob(options: UseUploadJobOptions = {}): UseUploadJobRes
         return;
       }
     },
-    [setCompletedJob],
+    [
+      setCompletedJob,
+      setCurrentBatch,
+      setTotalBatches,
+      setBatchState,
+      setIsBatchProcessing,
+      batchState,
+    ],
   );
 
   const sseUrl = useMemo(

From 7cd2158b28d452526070ec9deda5e23234fd11a4 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:22:09 -0700
Subject: [PATCH 160/173] Frontend: Add PerformanceSection to Settings

---
 frontend/src/pages/SettingsPage.tsx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/frontend/src/pages/SettingsPage.tsx b/frontend/src/pages/SettingsPage.tsx
index cf2a901..dfe8055 100644
--- a/frontend/src/pages/SettingsPage.tsx
+++ b/frontend/src/pages/SettingsPage.tsx
@@ -1,6 +1,7 @@
 import { useEffect } from "react";
 import CacheSection from "../components/settings/CacheSection.tsx";
 import DangerZone from "../components/settings/DangerZone.tsx";
+import PerformanceSection from "../components/settings/PerformanceSection.tsx";
 import SettingsForm from "../components/settings/SettingsForm.tsx";
 import UpdateSection from "../components/settings/UpdateSection.tsx";
 import { useAppStore } from "../stores/appStore.ts";
@@ -24,6 +25,7 @@ export default function SettingsPage() {
     <div className="max-w-3xl mx-auto space-y-6">
       <h2 className="text-xl font-semibold text-nlr-text">Settings</h2>
       <SettingsForm />
+      <PerformanceSection />
       <UpdateSection />
       <CacheSection />
       <DangerZone />

From 043b910e7e958f8993a24a5e1a615909de6b8e5d Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:22:46 -0700
Subject: [PATCH 161/173] Frontend: Wire in batching to upload page

---
 frontend/src/pages/UploadPage.tsx | 162 ++++++++++++++++++++++--------
 1 file changed, 120 insertions(+), 42 deletions(-)

diff --git a/frontend/src/pages/UploadPage.tsx b/frontend/src/pages/UploadPage.tsx
index 6f27c7d..d4ff7a4 100644
--- a/frontend/src/pages/UploadPage.tsx
+++ b/frontend/src/pages/UploadPage.tsx
@@ -6,14 +6,17 @@
  *   with phase-aware header, toolbar, and footer.
  */
 
-import { useCallback, useEffect, useMemo, useRef, useState } from "react";
+import { useCallback, useEffect, useMemo, useState } from "react";
 
 import Spinner from "../components/common/Spinner.tsx";
+import ActiveFilesList from "../components/upload/ActiveFilesList.tsx";
+import BatchProgress from "../components/upload/BatchProgress.tsx";
 import CancelConfirmModal from "../components/upload/CancelConfirmModal.tsx";
 import ConfirmModal from "../components/upload/ConfirmModal.tsx";
 import FolderBrowser from "../components/upload/FolderBrowser.tsx";
 import type { FolderExclusions } from "../components/upload/FolderBrowser.tsx";
 import ReviewToolbar, { StatusFilterBar } from "../components/upload/ReviewToolbar.tsx";
+import ScanProgressModal from "../components/upload/ScanProgressModal.tsx";
 import Stepper from "../components/upload/Stepper.tsx";
 import UnifiedFileTable from "../components/upload/UnifiedFileTable.tsx";
 import UploadFooter from "../components/upload/UploadFooter.tsx";
@@ -34,8 +37,9 @@ export default function UploadPage() {
     folderPath,
     setFolderPath,
     scanFolders,
-    scanTotals,
     completedJob,
+    batchState,
+    isBatchProcessing,
     reset,
   } = useUploadStore();
 
@@ -47,6 +51,7 @@ export default function UploadPage() {
     isScanning,
     scanComplete,
     folders,
+    foldersTotal,
     totals,
   } = useFolderScan();
 
@@ -89,29 +94,21 @@ export default function UploadPage() {
   const [pendingSelectedPaths, setPendingSelectedPaths] = useState<string[]>([]);
   const [selectedPaths, setSelectedPaths] = useState<Set<string>>(new Set());
 
+  // Delay scan modal by 500 ms — fast/cached scans complete before the timer
+  // fires, so the modal never flashes for them.
+  const [showScanModal, setShowScanModal] = useState(false);
+  useEffect(() => {
+    if (!isScanning) {
+      setShowScanModal(false);
+      return;
+    }
+    const timer = setTimeout(() => setShowScanModal(true), 500);
+    return () => clearTimeout(timer);
+  }, [isScanning]);
+
   // Derive phase from step
   const phase: UploadPhase = step <= 2 ? "review" : step === 3 ? "uploading" : "summary";
 
-  // ── Sync FileStore from scan data as folders arrive ──
-
-  const prevFoldersRef = useRef(folders);
-  if (folders !== prevFoldersRef.current) {
-    prevFoldersRef.current = folders;
-    if (folders.length > 0 && step >= 2) {
-      store.buildFromScan(folders);
-      // Auto-select new files
-      const newSelected = new Set<string>();
-      for (const folder of folders) {
-        for (const file of folder.files) {
-          if (!file.already_uploaded) {
-            newSelected.add(file.path);
-          }
-        }
-      }
-      setSelectedPaths(newSelected);
-    }
-  }
-
   // ── Freeze/unfreeze sort on phase transitions ──
 
   useEffect(() => {
@@ -121,17 +118,40 @@ export default function UploadPage() {
 
   // ── Step transitions ──
 
-  /** Step 1 -> 2: User selected a folder. Start scanning and advance. */
+  /** Step 1: User selected a folder. Start scanning (stay on Step 1 while scanning). */
   const handleFolderSelected = useCallback(
     async (path: string, exclusions?: FolderExclusions) => {
       store.clear();
       setFolderPath(path);
-      setStep(2);
+      // Stay on Step 1 while scanning - auto-advance when complete
       await startScan(path, false, exclusions);
     },
-    [setFolderPath, setStep, startScan, store],
+    [setFolderPath, startScan, store],
   );
 
+  /** Auto-advance to Step 2 when scan completes.
+   *
+   * We populate the FileStore here, right before advancing, because by the time
+   * scanComplete becomes true the folders array reference has already settled —
+   * any render-time ref-comparison trick would have already consumed the change
+   * while step was still 1 and skipped the buildFromScan call.
+   */
+  useEffect(() => {
+    if (step === 1 && scanComplete && folders.length > 0) {
+      store.buildFromScan(folders);
+      const newSelected = new Set<string>();
+      for (const folder of folders) {
+        for (const file of folder.files) {
+          if (!file.already_uploaded) {
+            newSelected.add(file.path);
+          }
+        }
+      }
+      setSelectedPaths(newSelected);
+      setStep(2);
+    }
+  }, [step, scanComplete, folders, store, setSelectedPaths, setStep]);
+
   /** Step 2: User clicks "Start Upload" — show confirmation modal. */
   const handleStartUploadClick = useCallback(() => {
     setPendingSelectedPaths(Array.from(selectedPaths));
@@ -180,6 +200,15 @@ export default function UploadPage() {
     reset();
   }, [reset, store]);
 
+  /** Cancel scan and return to Step 1 if needed. */
+  const handleCancelScan = useCallback(async () => {
+    await cancelScan();
+    // If we're on a later step during scan (shouldn't happen with new flow, but handle it)
+    if (step > 1) {
+      setStep(1);
+    }
+  }, [cancelScan, step, setStep]);
+
   /** Back from step 2 -> step 1. */
   const handleBack = useCallback(async () => {
     if (isScanning) {
@@ -291,9 +320,30 @@ export default function UploadPage() {
     downloadUploadCsv(Array.from(store.getAllRows().values()), jobId);
   }, [completedJob, store]);
 
-  // ── Active totals for header ──
-
-  const activeTotals = scanComplete ? totals : scanTotals;
+  // ── Review KPIs: what is actually going to happen when the user clicks Upload ──
+  //
+  // toUpload    — new selected files (will be sent to S3)
+  // uploadSize  — bytes of those new files
+  // alreadyOnS3 — selected files already there (will be skipped)
+  // totalInFolder — all files found in the scan (context denominator)
+  const activeTotals = useMemo(() => {
+    let toUpload = 0;
+    let uploadSize = 0;
+    let alreadyOnS3 = 0;
+    for (const file of allFiles) {
+      if (selectedPaths.has(file.path)) {
+        if (file.alreadyUploaded) {
+          alreadyOnS3++;
+        } else {
+          toUpload++;
+          uploadSize += file.size;
+        }
+      }
+    }
+    return { toUpload, uploadSize, alreadyOnS3, totalInFolder: allFiles.length };
+  // `files` dep ensures we recompute when the store snapshot changes
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [allFiles, selectedPaths, files]);
 
   // ── Render ──
 
@@ -371,20 +421,36 @@ export default function UploadPage() {
             />
           )}
 
-          {/* The unified file table — stays mounted across phases */}
-          <UnifiedFileTable
-            phase={phase}
-            files={files}
-            sortKey={store.getSortKey()}
-            sortDir={store.getSortDir()}
-            onSort={(key) => store.setSort(key)}
-            isSortFrozen={store.isFrozen()}
-            selectedPaths={selectedPaths}
-            onToggleFile={toggleFile}
-            onToggleAllFiltered={toggleAllFiltered}
-            headerChecked={headerChecked}
-            headerIndeterminate={headerIndeterminate}
-          />
+          {/* Batch processing UI for upload phase with large jobs */}
+          {phase === "uploading" && isBatchProcessing ? (
+            <>
+              <BatchProgress
+                batchState={batchState}
+                jobProgressPercent={uploadJob.progressPercent}
+                jobFilesCompleted={uploadJob.filesProcessed}
+                jobFilesTotal={uploadJob.totalFiles}
+                jobFilesUploaded={uploadJob.statusCounts.uploaded}
+                jobFilesFailed={uploadJob.statusCounts.failed}
+                isRunning={uploadJob.isRunning}
+              />
+              <ActiveFilesList files={uploadJob.activeFiles} />
+            </>
+          ) : (
+            /* The unified file table — stays mounted across phases */
+            <UnifiedFileTable
+              phase={phase}
+              files={files}
+              sortKey={store.getSortKey()}
+              sortDir={store.getSortDir()}
+              onSort={(key) => store.setSort(key)}
+              isSortFrozen={store.isFrozen()}
+              selectedPaths={selectedPaths}
+              onToggleFile={toggleFile}
+              onToggleAllFiltered={toggleAllFiltered}
+              headerChecked={headerChecked}
+              headerIndeterminate={headerIndeterminate}
+            />
+          )}
 
           {/* Bottom action buttons */}
           <UploadFooter
@@ -432,6 +498,18 @@ export default function UploadPage() {
           )}
         </div>
       )}
+
+      {/* Scan progress modal - only shown after 500 ms delay so fast/cached
+          scans never flash the modal at all. */}
+      <ScanProgressModal
+        isOpen={showScanModal && !showConfirmModal}
+        foldersScanned={folders.length}
+        foldersTotal={foldersTotal}
+        totalFiles={totals.totalFiles}
+        totalSize={totals.totalSize}
+        folderPath={folderPath}
+        onCancel={handleCancelScan}
+      />
     </div>
   );
 }

From 1a0f3ade9e80b68037af32470eb09c22edab0323 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:23:10 -0700
Subject: [PATCH 162/173] Frontend: Add batching support to uploadStore

---
 frontend/src/stores/uploadStore.ts | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/frontend/src/stores/uploadStore.ts b/frontend/src/stores/uploadStore.ts
index 5efb416..cc48b63 100644
--- a/frontend/src/stores/uploadStore.ts
+++ b/frontend/src/stores/uploadStore.ts
@@ -1,5 +1,5 @@
 import { create } from "zustand";
-import type { ScannedFolder, UploadJob } from "../types/api.ts";
+import type { BatchState, ScannedFolder, UploadJob } from "../types/api.ts";
 
 export type UploadStep = 1 | 2 | 3 | 4;
 
@@ -17,6 +17,7 @@ interface UploadState {
   scanFolders: ScannedFolder[];
   scanComplete: boolean;
   isScanning: boolean;
+  scanFoldersTotal: number;
   scanTotals: {
     totalFiles: number;
     alreadyUploaded: number;
@@ -26,6 +27,7 @@ interface UploadState {
   addScanFolder: (folder: ScannedFolder) => void;
   setScanComplete: (complete: boolean) => void;
   setIsScanning: (scanning: boolean) => void;
+  setScanFoldersTotal: (total: number) => void;
   updateScanTotals: (totals: { totalFiles: number; alreadyUploaded: number; totalSize: number }) => void;
 
   // Upload job
@@ -34,6 +36,16 @@ interface UploadState {
   setUploadJobId: (id: string | null) => void;
   setCompletedJob: (job: UploadJob | null) => void;
 
+  // Batch processing state
+  currentBatch: number | null;
+  totalBatches: number | null;
+  batchState: BatchState | null;
+  isBatchProcessing: boolean;
+  setCurrentBatch: (batch: number | null) => void;
+  setTotalBatches: (batches: number | null) => void;
+  setBatchState: (state: BatchState | null) => void;
+  setIsBatchProcessing: (processing: boolean) => void;
+
   // Reset
   reset: () => void;
 }
@@ -45,9 +57,14 @@ const initialState = {
   scanFolders: [],
   scanComplete: false,
   isScanning: false,
+  scanFoldersTotal: 0,
   scanTotals: { totalFiles: 0, alreadyUploaded: 0, totalSize: 0 },
   uploadJobId: null,
   completedJob: null,
+  currentBatch: null,
+  totalBatches: null,
+  batchState: null,
+  isBatchProcessing: false,
 };
 
 export const useUploadStore = create<UploadState>((set) => ({
@@ -61,10 +78,16 @@ export const useUploadStore = create<UploadState>((set) => ({
     set((s) => ({ scanFolders: [...s.scanFolders, folder] })),
   setScanComplete: (scanComplete) => set({ scanComplete }),
   setIsScanning: (isScanning) => set({ isScanning }),
+  setScanFoldersTotal: (scanFoldersTotal) => set({ scanFoldersTotal }),
   updateScanTotals: (scanTotals) => set({ scanTotals }),
 
   setUploadJobId: (uploadJobId) => set({ uploadJobId }),
   setCompletedJob: (completedJob) => set({ completedJob }),
 
+  setCurrentBatch: (currentBatch) => set({ currentBatch }),
+  setTotalBatches: (totalBatches) => set({ totalBatches }),
+  setBatchState: (batchState) => set({ batchState }),
+  setIsBatchProcessing: (isBatchProcessing) => set({ isBatchProcessing }),
+
   reset: () => set(initialState),
 }));

From bd74dc4289d82b29078ada3f543d619635d2dfb4 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:23:41 -0700
Subject: [PATCH 163/173] Frontend: Add batching and performance types

---
 frontend/src/types/api.ts | 84 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

diff --git a/frontend/src/types/api.ts b/frontend/src/types/api.ts
index a2e6d2f..fb71ea2 100644
--- a/frontend/src/types/api.ts
+++ b/frontend/src/types/api.ts
@@ -117,6 +117,90 @@ export interface AutoUploadStartingEvent {
   job_id: string;
 }
 
+// ── Batch processing types ──
+
+export interface BatchProcessingSettings {
+  enabled: boolean;
+  batch_size: number;
+  auto_tune_workers: boolean;
+  max_workers: number;
+  target_cpu_percent: number;
+  skip_mcap_validation: boolean;
+  use_database_for_large_jobs: boolean;
+  large_job_threshold: number;
+}
+
+export interface BatchState {
+  batch_id: number;
+  total_batches: number;
+  files_in_batch: number;
+  status: "pending" | "processing" | "completed" | "failed" | "cancelled";
+  files_processed: number;
+  files_uploaded: number;
+  files_failed: number;
+  bytes_uploaded: number;
+  started_at: string | null;
+  completed_at: string | null;
+  duration_seconds: number | null;
+  error_message: string;
+}
+
+export interface BatchStartedEvent {
+  type: "batch_started";
+  batch_id: number;
+  total_batches: number;
+  files_in_batch: number;
+}
+
+export interface BatchProgressEvent {
+  type: "batch_progress";
+  batch_id: number;
+  active_files: FileUploadState[]; // Max 8 items
+  batch_files_completed: number;
+  batch_files_total: number;
+  job_files_completed: number;
+  job_files_total: number;
+  job_progress_percent: number;
+}
+
+export interface BatchCompletedEvent {
+  type: "batch_completed";
+  batch_id: number;
+  files_uploaded: number;
+  files_failed: number;
+}
+
+export interface JobCompletedEvent {
+  type: "job_completed";
+  job_id: string;
+  status: "completed" | "failed" | "cancelled";
+  total_files: number;
+  files_uploaded: number;
+  files_failed: number;
+  duration_seconds: number;
+}
+
+export interface PaginatedResults {
+  job_id: string;
+  files: FileUploadState[];
+  pagination: {
+    page: number;
+    per_page: number;
+    total_files: number;
+    total_pages: number;
+    has_next: boolean;
+    has_prev: boolean;
+  };
+  job_metadata: {
+    job_id: string;
+    status: string;
+    total_files: number;
+    files_uploaded: number;
+    files_failed: number;
+    total_bytes: number;
+  };
+}
+
 // ── Scan types ──
 
 export interface ScannedFileInfo {

From e102fd6c51b903fa7079ecbf2c76a50618e37df0 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:24:18 -0700
Subject: [PATCH 164/173] Frontend: Add settings provenance types

---
 frontend/src/types/api.ts | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/frontend/src/types/api.ts b/frontend/src/types/api.ts
index fb71ea2..a753444 100644
--- a/frontend/src/types/api.ts
+++ b/frontend/src/types/api.ts
@@ -332,6 +332,16 @@ export interface S3Breadcrumb {
 
 // ── Settings types ──
 
+export type ValueSourceType = "builtin" | "default_file" | "settings_file" | "env";
+
+export interface ValueSource {
+  source: ValueSourceType;
+  /** Absolute path to the file (present for default_file and settings_file). */
+  path?: string;
+  /** Environment variable name (present for env). */
+  env_var?: string;
+}
+
 export interface AppSettings {
   aws_profile: string;
   aws_region: string;
@@ -339,6 +349,9 @@ export interface AppSettings {
   default_upload_folder: string;
   display_name: string;
   log_directory: string;
+  batch_processing?: BatchProcessingSettings;
+  /** Provenance metadata returned by the API — not sent on PUT. */
+  value_sources?: Record<string, ValueSource>;
 }
 
 export interface VersionInfo {

From 1065310bb37b56486ce501e008f941f1b9519c6b Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:24:38 -0700
Subject: [PATCH 165/173] Settings: Add default batch processing settings

---
 settings.default.json | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/settings.default.json b/settings.default.json
index 7b271cb..a633a92 100644
--- a/settings.default.json
+++ b/settings.default.json
@@ -3,5 +3,15 @@
     "aws_region": "us-west-2",
     "s3_bucket": "",
     "default_upload_folder": "",
-    "log_directory": "logs"
+    "log_directory": "logs",
+    "batch_processing": {
+        "enabled": true,
+        "batch_size": 100,
+        "auto_tune_workers": true,
+        "max_workers": 4,
+        "target_cpu_percent": 70.0,
+        "skip_mcap_validation": false,
+        "use_database_for_large_jobs": true,
+        "large_job_threshold": 1000
+    }
 }

From 79d1dd167db74beef2a26036b157732f0b491c3f Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:24:57 -0700
Subject: [PATCH 166/173] Tests: Add logs and infra tests

---
 tests/test_log_service.py        |  32 ++-----
 tests/test_sse_infrastructure.py | 158 +++++++++++++++++++++++++++++++
 2 files changed, 166 insertions(+), 24 deletions(-)
 create mode 100644 tests/test_sse_infrastructure.py

diff --git a/tests/test_log_service.py b/tests/test_log_service.py
index 9f5c264..132f856 100644
--- a/tests/test_log_service.py
+++ b/tests/test_log_service.py
@@ -113,9 +113,7 @@ def test_error_convenience(self, log_service: LogService, _mock_settings: Any) -
         entry = json.loads(log_file.read_text().strip())
         assert entry["level"] == "ERROR"
 
-    def test_multiple_entries_appended(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_multiple_entries_appended(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that multiple log calls append to the same file."""
         with _mock_settings:
             log_service.info("app", "event1", "First")
@@ -127,9 +125,7 @@ def test_multiple_entries_appended(
         lines = [line for line in log_file.read_text().strip().split("\n") if line]
         assert len(lines) == 3
 
-    def test_no_metadata_omits_field(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_no_metadata_omits_field(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that metadata field is omitted when not provided."""
         with _mock_settings:
             log_service.info("app", "test", "No metadata")
@@ -206,9 +202,7 @@ def test_read_entries_date_filter_hive(
         assert result["total"] == 1
         assert result["entries"][0]["event"] == "event1"
 
-    def test_read_entries_invalid_date(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_read_entries_invalid_date(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that an invalid date returns empty results."""
         with _mock_settings:
             result = log_service.read_log_entries(date="not-a-date")
@@ -284,9 +278,7 @@ def test_empty_stats(self, log_service: LogService, _mock_settings: Any) -> None
         assert stats["total_entries"] == 0
         assert stats["file_count"] == 0
 
-    def test_stats_includes_csv_count(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_stats_includes_csv_count(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that stats include csv_count."""
         with _mock_settings:
             log_service.info("app", "test", "Entry")
@@ -386,9 +378,7 @@ def test_extract_date_from_non_hive_path(self) -> None:
         result = LogService._extract_date_from_hive_path(path)
         assert result is None
 
-    def test_log_writes_to_hive_path(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_log_writes_to_hive_path(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that log() writes to a hive-partitioned events.jsonl."""
         log_dir: Path = log_service._test_settings_mock.log_directory  # type: ignore[attr-defined]
 
@@ -471,9 +461,7 @@ def _make_mock_job(self) -> MagicMock:
         mock_job.files = [mock_file]
         return mock_job
 
-    def test_save_job_csv_creates_file(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_save_job_csv_creates_file(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that save_job_csv creates a CSV at the correct hive path."""
         log_dir: Path = log_service._test_settings_mock.log_directory  # type: ignore[attr-defined]
         job_id = "a1b2c3d4-5678-9abc-def0-1234567890ab"
@@ -489,9 +477,7 @@ def test_save_job_csv_creates_file(
         assert result_path.name.endswith(".csv")
         assert result_path.exists()
 
-    def test_save_job_csv_columns(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_save_job_csv_columns(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that the CSV has all 14 expected columns."""
         job_id = "test-job-id-1234"
         completed_at = datetime(2026, 2, 8, 12, 0, 0, tzinfo=UTC)
@@ -522,9 +508,7 @@ def test_save_job_csv_columns(
         ]
         assert header == expected_columns
 
-    def test_save_job_csv_data_row(
-        self, log_service: LogService, _mock_settings: Any
-    ) -> None:
+    def test_save_job_csv_data_row(self, log_service: LogService, _mock_settings: Any) -> None:
         """Test that the CSV has a data row for each file."""
         job_id = "test-job-id"
         completed_at = datetime(2026, 2, 8, 12, 0, 0, tzinfo=UTC)
diff --git a/tests/test_sse_infrastructure.py b/tests/test_sse_infrastructure.py
new file mode 100644
index 0000000..e608457
--- /dev/null
+++ b/tests/test_sse_infrastructure.py
@@ -0,0 +1,158 @@
+"""Tests for SSE infrastructure: event signaling, queue management, and resource cleanup."""
+
+import threading
+import time
+from collections.abc import Generator
+from typing import Any
+
+import pytest
+
+from app.routes.upload import (
+    SSE_QUEUE_TTL_SECONDS,
+    _cleanup_old_sse_queues,
+    _sse_events,
+    _sse_queues,
+    _sse_timestamps,
+    send_sse_event,
+)
+
+
+@pytest.fixture
+def clear_sse_state() -> Generator[None, None, None]:
+    """Clear SSE module state before each test."""
+    _sse_queues.clear()
+    _sse_events.clear()
+    _sse_timestamps.clear()
+    yield
+    _sse_queues.clear()
+    _sse_events.clear()
+    _sse_timestamps.clear()
+
+
+def test_send_sse_event_creates_timestamp(clear_sse_state: Any) -> None:
+    """Test that sending an event updates the timestamp."""
+    from collections import deque
+
+    job_id = "test-job-123"
+
+    # Create a queue manually
+    queue = deque()
+    _sse_queues[job_id] = [queue]
+
+    # Send event
+    send_sse_event(job_id, {"type": "test", "data": "hello"})
+
+    # Verify timestamp was created
+    assert job_id in _sse_timestamps
+    assert time.time() - _sse_timestamps[job_id] < 1  # Within 1 second
+
+
+def test_send_sse_event_signals_waiting_threads(clear_sse_state: Any) -> None:
+    """Test that sending an event signals the threading.Event."""
+    from collections import deque
+
+    job_id = "test-job-456"
+
+    # Create queue and event
+    queue = deque()
+    event = threading.Event()
+    _sse_queues[job_id] = [queue]
+    _sse_events[job_id] = event
+
+    # Event should not be set initially
+    assert not event.is_set()
+
+    # Send event
+    send_sse_event(job_id, {"type": "test"})
+
+    # Event should now be set
+    assert event.is_set()
+    assert len(queue) == 1
+
+
+def test_cleanup_removes_old_queues(clear_sse_state: Any) -> None:
+    """Test that cleanup removes expired queues."""
+    from collections import deque
+
+    # Create some queues with old timestamps
+    old_time = time.time() - SSE_QUEUE_TTL_SECONDS - 100
+    recent_time = time.time()
+
+    _sse_queues["old-job-1"] = [deque()]
+    _sse_timestamps["old-job-1"] = old_time
+    _sse_events["old-job-1"] = threading.Event()
+
+    _sse_queues["old-job-2"] = [deque()]
+    _sse_timestamps["old-job-2"] = old_time
+
+    _sse_queues["recent-job"] = [deque()]
+    _sse_timestamps["recent-job"] = recent_time
+
+    # Run cleanup
+    removed = _cleanup_old_sse_queues()
+
+    # Should remove 2 old jobs, keep recent one
+    assert removed == 2
+    assert "old-job-1" not in _sse_queues
+    assert "old-job-1" not in _sse_events
+    assert "old-job-1" not in _sse_timestamps
+    assert "old-job-2" not in _sse_queues
+    assert "recent-job" in _sse_queues
+
+
+def test_cleanup_with_no_expired_queues(clear_sse_state: Any) -> None:
+    """Test that cleanup does nothing when all queues are recent."""
+    from collections import deque
+
+    recent_time = time.time()
+
+    _sse_queues["job-1"] = [deque()]
+    _sse_timestamps["job-1"] = recent_time
+
+    _sse_queues["job-2"] = [deque()]
+    _sse_timestamps["job-2"] = recent_time
+
+    # Run cleanup
+    removed = _cleanup_old_sse_queues()
+
+    # Should remove nothing
+    assert removed == 0
+    assert len(_sse_queues) == 2
+
+
+def test_event_driven_signaling(clear_sse_state: Any) -> None:
+    """Test that Event.wait() is more efficient than polling."""
+    from collections import deque
+
+    job_id = "test-job-signal"
+    queue = deque()
+    event = threading.Event()
+
+    _sse_queues[job_id] = [queue]
+    _sse_events[job_id] = event
+
+    # Simulate waiting thread
+    wait_result: list[float] = []
+
+    def waiter() -> None:
+        # This should block until event is set
+        start = time.time()
+        event.wait(timeout=2.0)
+        elapsed = time.time() - start
+        wait_result.append(elapsed)
+
+    thread = threading.Thread(target=waiter)
+    thread.start()
+
+    # Small delay to ensure thread is waiting
+    time.sleep(0.1)
+
+    # Send event to wake thread
+    send_sse_event(job_id, {"type": "wake"})
+
+    # Wait for thread to finish
+    thread.join(timeout=3.0)
+
+    # Thread should have woken up quickly (< 0.5s, not 2s timeout)
+    assert len(wait_result) == 1
+    assert wait_result[0] < 0.5  # Should be nearly instant

From 792d3f710575eb6c4977e4302c97c5cf02f6ac72 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 07:25:30 -0700
Subject: [PATCH 167/173] Backend: Add sse registry/cleanup to init.py

---
 app/__init__.py | 51 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/app/__init__.py b/app/__init__.py
index aaa06e4..d418c3a 100644
--- a/app/__init__.py
+++ b/app/__init__.py
@@ -1,11 +1,56 @@
 """Flask application factory for MCAP S3 Uploader."""
 
+import atexit
 import os
+import threading
 
 from flask import Flask
 
 from app.config import get_package_version, get_settings
 
+# Background cleanup thread control
+_cleanup_thread: threading.Thread | None = None
+_cleanup_stop_event = threading.Event()
+
+
+def _sse_cleanup_worker() -> None:
+    """Background worker that periodically cleans up stale SSE queues."""
+    from app.routes.upload import _cleanup_old_sse_queues
+
+    while not _cleanup_stop_event.wait(timeout=300):  # Check every 5 minutes
+        try:
+            removed = _cleanup_old_sse_queues()
+            if removed > 0:
+                from app.services.log_service import get_log_service
+
+                log = get_log_service()
+                log.info(
+                    "sse",
+                    "sse_cleanup",
+                    f"Cleaned up {removed} stale SSE queues",
+                    {"queues_removed": removed},
+                )
+        except Exception:
+            # Don't crash the cleanup thread on errors
+            pass
+
+
+def _start_sse_cleanup() -> None:
+    """Start the background SSE cleanup thread."""
+    global _cleanup_thread
+    if _cleanup_thread is None:
+        _cleanup_thread = threading.Thread(
+            target=_sse_cleanup_worker, daemon=True, name="SSECleanup"
+        )
+        _cleanup_thread.start()
+
+
+def _stop_sse_cleanup() -> None:
+    """Stop the background SSE cleanup thread."""
+    _cleanup_stop_event.set()
+    if _cleanup_thread:
+        _cleanup_thread.join(timeout=2.0)
+
 
 def create_app() -> Flask:
     """Create and configure the Flask application."""
@@ -39,6 +84,12 @@ def inject_display_name() -> dict[str, str]:
     app.register_blueprint(logs_bp, url_prefix="/api/logs")
     app.register_blueprint(delete_bp, url_prefix="/api/delete")
 
+    # Start background SSE cleanup thread
+    _start_sse_cleanup()
+
+    # Register cleanup on shutdown
+    atexit.register(_stop_sse_cleanup)
+
     # Log application startup
     from app.services.log_service import get_log_service
 

From c513777e29cb45bf59cad4a5d84321732f2104c2 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 09:04:14 -0700
Subject: [PATCH 168/173] Fix: Don't cancel futures

---
 app/services/upload_manager.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/services/upload_manager.py b/app/services/upload_manager.py
index 849b9bb..2237018 100644
--- a/app/services/upload_manager.py
+++ b/app/services/upload_manager.py
@@ -1367,8 +1367,8 @@ def byte_callback(uploaded: int, total: int) -> None:
                 {"job_id": job_id, "error": str(e)},
             )
         finally:
-            # Wait for in-flight uploads; cancel_work_items prevents queued tasks from starting
-            upload_executor.shutdown(wait=True, cancel_futures=True)
+            # Wait for ALL uploads (in-flight + queued) to complete
+            upload_executor.shutdown(wait=True)
 
             # Mark any files still in non-terminal states as cancelled
             if job.cancelled:

From 862b489faa1314144d79a111730baa73e61dd859 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 09:37:34 -0700
Subject: [PATCH 169/173] Actions: Set js tests working dir to frontend

---
 .github/workflows/run_tests.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 5e7bb19..6b3b087 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -62,9 +62,12 @@ jobs:
         with:
           node-version: 22
           cache: npm
+          cache-dependency-path: frontend/package-lock.json
 
       - name: Install dependencies
         run: npm ci
+        working-directory: frontend
 
       - name: Lint, type check, and test
         run: npm run check
+        working-directory: frontend

From 732b1e003d54497d4578ec556fddd6a19b7fb980 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 09:37:52 -0700
Subject: [PATCH 170/173] Pre Commit: Skip json files with comments

---
 .pre-commit-config.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 924d336..24add70 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,6 +9,7 @@ repos:
       - id: check-merge-conflict
       - id: check-yaml
       - id: check-json
+        exclude: ^frontend/tsconfig\.
       - id: no-commit-to-branch
         args: [--branch, main]
 

From 4f6ccc3cb566d280e73fbfff796eb9b3707a61c3 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 09:38:08 -0700
Subject: [PATCH 171/173] Dev: Add psutil type stubs

---
 requirements-dev.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index 1b738ee..8a9e9e5 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -2,6 +2,7 @@ pytest>=8.0.0
 pytest-cov>=4.1.0
 moto[s3]>=5.0.0
 mypy>=1.8.0
+types-psutil>=5.9.0
 boto3-stubs[s3]>=1.34.0
 ruff>=0.2.0
 pre-commit>=3.6.0

From 210d152e266ee6a817ddb2f3322ccc2094e93444 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 09:39:06 -0700
Subject: [PATCH 172/173] Release: Bump to 1.0.0

---
 frontend/package.json | 2 +-
 pyproject.toml        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/frontend/package.json b/frontend/package.json
index 44356f3..2686499 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -1,7 +1,7 @@
 {
   "name": "frontend",
   "private": true,
-  "version": "0.0.0",
+  "version": "1.0.0",
   "type": "module",
   "scripts": {
     "dev": "vite",
diff --git a/pyproject.toml b/pyproject.toml
index 6670e02..fca511f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "modaq-upload"
-version = "0.2.2"
+version = "1.0.0"
 description = "Python/Flask web application for uploading MODAQ data to Amazon AWS S3 buckets"
 requires-python = ">=3.11"
 authors = [

From 355d68d4dc199b4849f4c886feff8f8ecbd9d1d0 Mon Sep 17 00:00:00 2001
From: "Simms, Andrew" <andrew.simms@nlr.gov>
Date: Mon, 2 Mar 2026 09:42:10 -0700
Subject: [PATCH 173/173] Tests: Add shell html index for flask to test against

---
 tests/conftest.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/conftest.py b/tests/conftest.py
index 0bf19e8..e3896aa 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -31,6 +31,17 @@ def app() -> Generator[Flask, None, None]:
         )
         temp_settings = f.name
 
+    # Ensure frontend/dist/index.html exists so SPA routes can serve it
+    from app.routes.main import FRONTEND_DIST
+
+    dist_created = False
+    index_path = os.path.join(FRONTEND_DIST, "index.html")
+    if not os.path.exists(index_path):
+        os.makedirs(FRONTEND_DIST, exist_ok=True)
+        dist_created = True
+        with open(index_path, "w") as f:
+            f.write('<!doctype html><html><body><div id="root"></div></body></html>')
+
     # Create the app (settings will be loaded from default)
     _ = SETTINGS_FILE  # Reference to avoid unused import warning
 
@@ -41,6 +52,8 @@ def app() -> Generator[Flask, None, None]:
 
     # Cleanup
     os.unlink(temp_settings)
+    if dist_created:
+        os.unlink(index_path)
 
 
 @pytest.fixture