diff --git a/apps/web/src/components/ChatView.tsx b/apps/web/src/components/ChatView.tsx
index 5afd6d8d4e0b..8c10ab23d43e 100644
--- a/apps/web/src/components/ChatView.tsx
+++ b/apps/web/src/components/ChatView.tsx
@@ -3673,9 +3673,9 @@ export default function ChatView(props: ChatViewProps) {
           : null,
     [multiRepoStatusRoots, gitStatusCwd],
   );
-  // The files panel and @-mention search span the folders a `.code-workspace`
-  // lists, while git surfaces stay on `repoRoots`. Null searches the
-  // worktree-aware cwd alone.
+  // The files panel, @-mention search and chat file links span the folders a
+  // `.code-workspace` lists, while git surfaces stay on `repoRoots`. Null
+  // searches the worktree-aware cwd alone.
   const workspaceFileQuery = useEnvironmentQuery(
     projectWorkspaceFile === null
       ? null
@@ -3685,6 +3685,12 @@ export default function ChatView(props: ChatViewProps) {
         }),
   );
   const workspaceFolders = workspaceFileQuery.data?.folders ?? null;
+  // The first read of the folder list has not settled. The files panel holds
+  // its tree until then, since the fallback roots can show unlisted folders.
+  const projectFileRootsPending =
+    projectWorkspaceFile !== null &&
+    workspaceFileQuery.data === null &&
+    workspaceFileQuery.error === null;
   const projectFileRoots = useMemo(
     () =>
       resolveProjectFileRoots({
@@ -3694,6 +3700,10 @@ export default function ChatView(props: ChatViewProps) {
       }),
     [workspaceFolders, activeProject?.repoRoots, threadWorktrees],
   );
+  const fileLinkRoots = useMemo(
+    () => projectFileRoots?.map(({ root }) => root),
+    [projectFileRoots],
+  );
   // Single-repo git query scoped to the anchor root, backing the branch-sync,
   // PR-checkout, and refresh flows; the multi-repo status/diff surfaces use
   // `vcsStatusGroups` below.
@@ -9787,6 +9797,8 @@ export default function ChatView(props: ChatViewProps) {
           keybindings={keybindings}
           availableEditors={availableEditors}
           roots={projectFileRoots ?? undefined}
+          rootsPending={projectFileRootsPending}
+          onRefreshRoots={workspaceFileQuery.refresh}
           relativePath={
             renderedRightPanelSurface.kind === "file"
               ? renderedRightPanelSurface.relativePath
@@ -10003,9 +10015,7 @@ export default function ChatView(props: ChatViewProps) {
                     ? (heldPaintContext?.markdownCwd ?? undefined)
                     : (gitCwd ?? undefined)
                 }
-                markdownRepoRoots={
-                  !paintOnlyDisplayedTimeline && isMultiRepo ? activeProject?.repoRoots : undefined
-                }
+                markdownRepoRoots={paintOnlyDisplayedTimeline ? undefined : fileLinkRoots}
                 resolvedTheme={resolvedTheme}
                 timestampFormat={timestampFormat}
                 workspaceRoot={
diff --git a/apps/web/src/components/files/FileBrowserPanel.tsx b/apps/web/src/components/files/FileBrowserPanel.tsx
index aad4dc69243b..8f2b131a234f 100644
--- a/apps/web/src/components/files/FileBrowserPanel.tsx
+++ b/apps/web/src/components/files/FileBrowserPanel.tsx
@@ -46,6 +46,8 @@ interface FileBrowserPanelProps {
   roots?: readonly ProjectFileRoot[] | undefined;
   onOpenFile: (relativePath: string, root?: string) => void;
   onRefreshSelectedFile?: () => void;
+  /** Re-resolves `roots`, so a refresh also picks up a changed root list. */
+  onRefreshRoots?: () => void;
   workspaceMutationId: string | null;
 }
 
@@ -117,6 +119,7 @@ export default function FileBrowserPanel({
   roots,
   onOpenFile,
   onRefreshSelectedFile,
+  onRefreshRoots,
   workspaceMutationId,
 }: FileBrowserPanelProps) {
   const { resolvedTheme } = useTheme();
@@ -439,6 +442,7 @@ export default function FileBrowserPanel({
     refresh();
     if (query.trim()) pathSearch.refresh();
     onRefreshSelectedFile?.();
+    onRefreshRoots?.();
   };
   useWorkspaceMutationRefresh({
     mutationId: workspaceMutationId,
diff --git a/apps/web/src/components/files/FilePreviewPanel.tsx b/apps/web/src/components/files/FilePreviewPanel.tsx
index 544b3a14580a..8688d5f943ae 100644
--- a/apps/web/src/components/files/FilePreviewPanel.tsx
+++ b/apps/web/src/components/files/FilePreviewPanel.tsx
@@ -107,6 +107,10 @@ interface FilePreviewPanelProps {
   revealRequestId: number;
   // Multi-root projects (#923): roots to list/group in the file tree.
   roots?: readonly ProjectFileRoot[] | undefined;
+  // True while `roots` is still being resolved; the file tree waits for it.
+  rootsPending?: boolean | undefined;
+  // Re-resolves `roots` from their source when the user refreshes the tree.
+  onRefreshRoots?: (() => void) | undefined;
   // Owning root of the currently-open file. Reads/writes resolve against this
   // root (it may be a different repo than the anchor `cwd`). Null = anchor.
   fileRoot?: string | null | undefined;
@@ -929,6 +933,8 @@ export default function FilePreviewPanel({
   revealLine,
   revealRequestId,
   roots,
+  rootsPending,
+  onRefreshRoots,
   fileRoot,
   onOpenFile,
   onPendingChange,
@@ -1320,21 +1326,24 @@ export default function FilePreviewPanel({
           >
             {/* The tree caches folders by label, so a root that changes path under
                 the same label must remount it rather than show the old contents. */}
-            <FileBrowserPanel
-              key={`${environmentId}:${cwd}:${projectFileRootsKey(roots)}`}
-              environmentId={environmentId}
-              cwd={cwd}
-              projectName={projectName}
-              selectedPath={relativePath}
-              selectedRoot={fileRoot ?? undefined}
-              selectedPathRevealId={revealRequestId}
-              roots={roots}
-              onOpenFile={onOpenFile}
-              workspaceMutationId={workspaceMutationId}
-              {...(previewPath && !isMedia && !isPdf
-                ? { onRefreshSelectedFile: file.refresh }
-                : {})}
-            />
+            {rootsPending ? null : (
+              <FileBrowserPanel
+                key={`${environmentId}:${cwd}:${projectFileRootsKey(roots)}`}
+                environmentId={environmentId}
+                cwd={cwd}
+                projectName={projectName}
+                selectedPath={relativePath}
+                selectedRoot={fileRoot ?? undefined}
+                selectedPathRevealId={revealRequestId}
+                roots={roots}
+                onOpenFile={onOpenFile}
+                workspaceMutationId={workspaceMutationId}
+                {...(onRefreshRoots ? { onRefreshRoots } : {})}
+                {...(previewPath && !isMedia && !isPdf
+                  ? { onRefreshSelectedFile: file.refresh }
+                  : {})}
+              />
+            )}
           </aside>
         ) : null}
       </div>
diff --git a/apps/web/src/lib/projectFileRoots.test.ts b/apps/web/src/lib/projectFileRoots.test.ts
index 742eabb1f88f..7ce4224334f1 100644
--- a/apps/web/src/lib/projectFileRoots.test.ts
+++ b/apps/web/src/lib/projectFileRoots.test.ts
@@ -1,5 +1,6 @@
 import { describe, expect, it } from "vite-plus/test";
 
+import { resolveMarkdownFileLinkMeta } from "../markdown-links";
 import { resolveProjectFileRoots } from "./projectFileRoots";
 
 const folder = (absolutePath: string, exists = true) => ({ absolutePath, exists });
@@ -78,4 +79,30 @@ describe("resolveProjectFileRoots", () => {
     });
     expect(roots?.map((entry) => entry.label)).toEqual(["a/docs", "b/docs"]);
   });
+
+  // Chat file links are matched against these roots, so a link has to land on
+  // the root the panel lists the file under or the tree cannot highlight it.
+  it("claims chat links for nested, outside and worktree roots", () => {
+    const roots = paths(
+      resolveProjectFileRoots({
+        workspaceFolders: [folder("/ws/api"), folder("/ws/notes/2026"), folder("/elsewhere/notes")],
+        repoRoots: ["/ws/api"],
+        worktrees: [{ repoRoot: "/ws/api", worktreePath: "/wt/feature/api" }],
+      }),
+    );
+    const link = (path: string) =>
+      resolveMarkdownFileLinkMeta(path, "/ws", undefined, roots ?? undefined);
+    expect(link("/ws/notes/2026/plan.md")).toMatchObject({
+      fileRoot: "/ws/notes/2026",
+      workspaceRelativePath: "plan.md",
+    });
+    expect(link("/elsewhere/notes/todo.md")).toMatchObject({
+      fileRoot: "/elsewhere/notes",
+      workspaceRelativePath: "todo.md",
+    });
+    expect(link("/wt/feature/api/src/main.ts")).toMatchObject({
+      fileRoot: "/wt/feature/api",
+      workspaceRelativePath: "src/main.ts",
+    });
+  });
 });