[Draft] feat(cli): deterministically rebuild index.md from frontmatter

.skills/claude-history-ingest/SKILL.md

@@ -16,7 +16,7 @@ This skill can be invoked directly or via the `wiki-history-ingest` router (`/wi
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `CLAUDE_HISTORY_PATH` (defaults to `~/.claude`)
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), and `CLAUDE_HISTORY_PATH` (defaults to `~/.claude`)
 2. Read `.manifest.json` at the vault root to check what's already been ingested
 3. Read `index.md` at the vault root to know what the wiki already contains
 4. **Project Scoping** — read `WIKI_SKIP_PROJECTS` from config (comma-separated substrings). Exclude any project directory whose name contains one of them from **every** step below (scan, delta, sampling, manifest writes). If the user names extra projects to skip this run, add them. Apply the exclusion **once, uniformly** — don't hand-write `grep -v` filters into individual commands, which drifts between the scan and manifest steps.
@@ -411,6 +411,15 @@ Update `index.md` and `log.md` per the standard process:
 - [TIMESTAMP] CLAUDE_HISTORY_INGEST projects=N conversations=M desktop_sessions=D audit_logs=A pages_updated=X pages_created=Y mode=append|full
 ```
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 **`hot.md`** — Read `$OBSIDIAN_VAULT_PATH/hot.md` (create from the template in `wiki-ingest` if missing). Update **Recent Activity** with a one-line summary — e.g. "Ingested 5 Claude conversations across 2 projects; surfaced patterns in API design and testing strategy." Keep the last 3 operations. Update **Active Threads** if any ongoing project is now better understood. **Update the `updated:` field in the frontmatter** to the current timestamp — this is easy to forget; the body edit and the frontmatter bump must both happen.
 
 ## Privacy

.skills/codex-history-ingest/SKILL.md

@@ -16,7 +16,7 @@ This skill can be invoked directly or via the `wiki-history-ingest` router (`/wi
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `CODEX_HISTORY_PATH` (defaults to `~/.codex`)
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), and `CODEX_HISTORY_PATH` (defaults to `~/.codex`)
 2. Read `.manifest.json` at the vault root to check what has already been ingested
 3. Read `index.md` at the vault root to understand what the wiki already contains
 
@@ -196,6 +196,15 @@ Update `index.md` and `log.md`:
 - [TIMESTAMP] CODEX_HISTORY_INGEST sessions=N pages_updated=X pages_created=Y mode=append|full
 ```
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 **`hot.md`** — Read `$OBSIDIAN_VAULT_PATH/hot.md` (create from the template in `wiki-ingest` if missing). Update **Recent Activity** with a one-line summary — e.g. "Ingested 12 Codex sessions; surfaced recurring patterns in CLI tooling and shell scripting." Keep the last 3 operations. Update `updated` timestamp.
 
 ## Privacy and Compliance

.skills/copilot-history-ingest/SKILL.md

@@ -19,7 +19,7 @@ This skill can be invoked directly or via the `wiki-history-ingest` router (`/wi
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `COPILOT_HISTORY_PATH` (defaults to `~/.copilot/session-state`), and `COPILOT_VSCODE_STORAGE_PATH` (VS Code `workspaceStorage`; platform-specific — ask the user if absent)
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), `COPILOT_HISTORY_PATH` (defaults to `~/.copilot/session-state`), and `COPILOT_VSCODE_STORAGE_PATH` (VS Code `workspaceStorage`; platform-specific — ask the user if absent)
 2. Read `.manifest.json` at the vault root to check what's already been ingested
 3. Read `index.md` at the vault root to know what the wiki already contains
 
@@ -323,6 +323,15 @@ Update `index.md` and `log.md` per the standard process:
 - [TIMESTAMP] COPILOT_HISTORY_INGEST projects=N sessions=M checkpoints=C pages_updated=X pages_created=Y mode=append|full
 ```
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 **`hot.md`** — Read `$OBSIDIAN_VAULT_PATH/hot.md` (create from the template in `wiki-ingest` if missing). Update **Recent Activity** with a one-line summary — e.g. "Ingested 5 Copilot sessions across 2 projects; surfaced patterns in API design and testing strategy." Keep the last 3 operations. Update **Active Threads** if any ongoing project is now better understood. Update `updated` timestamp.
 
 ## Privacy

.skills/cross-linker/SKILL.md

@@ -218,6 +218,15 @@ To promote: move the page to `projects/<project-name>/references/` and update al
 - `_readouts/*` — derived readouts (wiki-narrate output)
 ```
 
+**`index.md`** — If link application or page promotion wrote visible files, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 ## Step 7: Update Log and Hot Cache
 
 Append to `log.md`:

.skills/daily-update/SKILL.md

@@ -14,7 +14,7 @@ You run a lightweight maintenance pass over the wiki: check source freshness, re
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `OBSIDIAN_WIKI_REPO`.
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), and `OBSIDIAN_WIKI_REPO`.
 2. **Derive vault-scoped state dir** — all runtime state is scoped to the resolved vault, not global:
    ```bash
    VAULT_ID=$(echo "$OBSIDIAN_VAULT_PATH" | md5sum 2>/dev/null | cut -c1-8 || md5 -q - <<< "$OBSIDIAN_VAULT_PATH" | cut -c1-8)
@@ -38,7 +38,14 @@ Compare each source in `.manifest.json` against its file's modification time. Cl
 
 **Step 2: Index refresh**
 
-Read `$OBSIDIAN_VAULT_PATH/index.md`. If any pages in the vault are missing from the index (or vice versa), update the index. Use `find $OBSIDIAN_VAULT_PATH -name "*.md" -not -path "*/_*"` to enumerate vault pages, then reconcile against the index.
+**`index.md`** — Run on every maintenance cycle:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
 
 **Step 3: hot.md update**
 

.skills/hermes-history-ingest/SKILL.md

@@ -16,7 +16,7 @@ This skill can be invoked directly or via the `wiki-history-ingest` router (`/wi
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `HERMES_HISTORY_PATH` (defaults to `~/.hermes`)
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), and `HERMES_HISTORY_PATH` (defaults to `~/.hermes`)
 2. Read `.manifest.json` at the vault root to check what has already been ingested
 3. Read `index.md` at the vault root to understand what the wiki already contains
 
@@ -187,6 +187,15 @@ Update `index.md` and `log.md`:
 - [TIMESTAMP] HERMES_HISTORY_INGEST memories=N sessions=M pages_updated=X pages_created=Y mode=append|full
 ```
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 **`hot.md`** — Read `$OBSIDIAN_VAULT_PATH/hot.md` (create from the template in `wiki-ingest` if missing). Update **Recent Activity** with a one-line summary — e.g. "Ingested 42 Hermes memories and 7 sessions; dominant themes: reasoning strategies, tool use patterns." Keep the last 3 operations. Update `updated` timestamp.
 
 ## Privacy and Compliance

.skills/llm-wiki/SKILL.md

@@ -129,6 +129,18 @@ A content-oriented catalog organized by category. Each entry has a one-line summ
 ❌ Don't: `description (#tag)` — breaks tag parsing
 ✅ Do: `description ( #tag)` — proper spacing and tag parsing
 
+### Deterministic Index Refresh
+
+After a workflow changes any visible wiki page's path, title, category, summary, or tags, rebuild the root index after all page writes succeed:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete. Do not use the manual fallback to hide a generator failure. Skip refresh during read-only, audit-only, dry-run, no-op, and staged-only flows that changed no visible page.
+
 ### `log.md`
 Chronological append-only record tracking every operation. Each entry is parseable:
 

.skills/openclaw-history-ingest/SKILL.md

@@ -16,7 +16,7 @@ This skill can be invoked directly or via the `wiki-history-ingest` router (`/wi
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `OPENCLAW_HISTORY_PATH` (defaults to `~/.openclaw`)
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), and `OPENCLAW_HISTORY_PATH` (defaults to `~/.openclaw`)
 2. Read `.manifest.json` at the vault root to check what has already been ingested
 3. Read `index.md` at the vault root to understand what the wiki already contains
 
@@ -205,6 +205,15 @@ Update `index.md` and `log.md`:
 - [TIMESTAMP] OPENCLAW_HISTORY_INGEST memory=updated daily_notes=N sessions=M pages_updated=X pages_created=Y mode=append|full
 ```
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 **`hot.md`** — Read `$OBSIDIAN_VAULT_PATH/hot.md` (create from the template in `wiki-ingest` if missing). Update **Recent Activity** with a one-line summary — e.g. "Ingested OpenClaw MEMORY.md and 14 daily notes; surfaced automation patterns and multi-agent coordination knowledge." Keep the last 3 operations. Update `updated` timestamp.
 
 ## Privacy and Compliance

.skills/pi-history-ingest/SKILL.md

@@ -18,7 +18,7 @@ This skill can be invoked directly or via the `wiki-history-ingest` router (`/wi
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `PI_HISTORY_PATH` (defaults to `~/.pi/agent/sessions`)
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`, `OBSIDIAN_LINK_FORMAT` (default `wikilink`), and `PI_HISTORY_PATH` (defaults to `~/.pi/agent/sessions`)
 2. Read `.manifest.json` at the vault root to check what has already been ingested
 3. Read `index.md` at the vault root to understand what the wiki already contains
 
@@ -260,6 +260,15 @@ Update `index.md` and `log.md`:
 - [TIMESTAMP] PI_HISTORY_INGEST sessions=N pages_updated=X pages_created=Y mode=append|full
 ```
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 **`hot.md`** — Read `$OBSIDIAN_VAULT_PATH/hot.md` (create from the template in `wiki-ingest` if missing). Update **Recent Activity** with a one-line summary — e.g. "Ingested 12 Pi sessions across 3 projects; surfaced patterns in CLI tooling and API design." Keep the last 3 operations. Update `updated` timestamp.
 
 ## Privacy and Compliance

.skills/tag-taxonomy/SKILL.md

@@ -15,7 +15,7 @@ You are enforcing consistent tagging across the wiki by normalizing tags to a co
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `OBSIDIAN_LINK_FORMAT` (default `wikilink`)
 2. Read `$OBSIDIAN_VAULT_PATH/_meta/taxonomy.md` — this is the canonical tag list
 3. Read `index.md` to understand the wiki's scope
 
@@ -142,6 +142,15 @@ For tags that aren't in the taxonomy and aren't aliases:
 
 If new canonical tags were agreed upon, append them to `_meta/taxonomy.md` in the correct section.
 
+**`index.md`** — Outside audit mode, if any visible page tags changed, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 ## Mode 3: Tagging a New Page
 
 When you're creating a wiki page and need to choose tags:

.skills/wiki-agent/SKILL.md

@@ -34,7 +34,7 @@ If no query is given, default to **recent sessions mode**: ingest the last 5 unp
 
 ## Before You Start
 
-1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH`.
+1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → `~/.obsidian-wiki/config` → prompt setup). This gives `OBSIDIAN_VAULT_PATH` and `OBSIDIAN_LINK_FORMAT` (default `wikilink`).
 2. Read `$OBSIDIAN_VAULT_PATH/.manifest.json` → know what's already ingested.
 3. Read `$OBSIDIAN_VAULT_PATH/hot.md` if it exists → warm context on recent wiki activity.
 
@@ -232,6 +232,15 @@ If a query was given but no relevant sessions were found, say so explicitly: "No
 
 ## Step 7: Update Tracking Files
 
+**`index.md`** — When pages were created or updated, after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete.
+
 Update `.manifest.json` for each session file processed:
 ```json
 {

.skills/wiki-capture/SKILL.md

@@ -228,7 +228,14 @@ Every note must link to at least 2 existing wiki pages. Search `index.md` before
 
 ## Step 6: Update Tracking Files
 
-**`index.md`** — Add the new page under its category section.
+**`index.md`** — Full Mode only: after all visible page writes succeed, run:
+
+```bash
+obsidian-wiki index "$OBSIDIAN_VAULT_PATH" --link-format "$OBSIDIAN_LINK_FORMAT"
+```
+
+If the `obsidian-wiki` executable is unavailable, manually reconcile `index.md` using the format in `llm-wiki/SKILL.md`.
+If the executable exists but the command fails, report the failure and stop before claiming bookkeeping is complete. Quick Mode remains excluded because it writes only to `_raw/`.
 
 **`log.md`** — Append:
 ```