Curator fixes

Wiki Curator — Checks & Fix Catalog (reference)

The supplemental diagnostic checks, the Phase 3 auto-fix catalog, and the Phase 4 judgment-fix procedure for claude-wiki-pages-curator-agent. The agent reads this skill during Phase 1 (diagnose) and Phases 3–4 (apply). Schema authority remains vault/CLAUDE.md; the contract, engine-heal preflight, severity classification, re-verify, report, and hard rules live in the agent body.

Supplemental checks (Phase 1.2 — not covered by the script)

Run each via Grep/Glob against vault/wiki/:

• Broken wikilinks — [[Target]] where Target matches neither any page's title: nor any entry in aliases:.
• Orphan pages — non-bookkeeping pages (excluding index.md, log.md, dashboard.md, folder notes, and legacy _index.md) with zero inbound wikilinks (index children: counts).
• Title collisions — two pages with the same title: → ambiguous wikilinks.
• Title missing from aliases — for every page: title must appear as the first entry in aliases (ghost-node prevention per vault/CLAUDE.md).
• Missing graph color groups — for each top-level topic folder (not _sources, _synthesis), check obsidian eval code="JSON.stringify(app.internalPlugins.plugins['graph'].instance.options.colorGroups)" for a matching path:wiki/<folder> query.
• Flat folder sprawl — any topic folder with > 12 direct .md children (excluding the folder's own index note).
• Excessive nesting — any folder deeper than 4 levels from wiki/.
• Stale confidence — pages with confidence < 0.5 and updated > 30 days ago.
• High confidence with single source — pages with type: entity | concept | synthesis where confidence ≥ 0.8 and sources: has only one entry.
• Ghost wikilinks in log.md — [[...]] targets in log entries that match no real page → should be replaced with backtick code formatting.

Heavier computational checks (Jaccard similarity for near-duplicate bodies, content-block deduplication) are not run from this agent. If the user wants them, extend verify-ingest.sh with --deep mode in a separate change.

Stale agent-session memories (no memory-specific auto-deletion)

A source_type: agent-session page in wiki/_sources/ is a first-class source note subject to the same lifecycle as every other source. The curator handles stale agent-session memories exactly like any stale page — there is no memory-specific deletion path, no separate staleness field, and no parallel staleness mechanism. The standard tools apply:

• status: stale + confidence — when an S4 WARN or 30-day calendar staleness finding targets a wiki page whose sources: list includes an agent-session source, the curator sets status: stale on the wiki page and may lower confidence, the same mutation it applies to any stale page.
• Agent-session source note itself — if the session source is unconfirmed past the staleness threshold or contradicted by newer sources, the curator sets status: stale on the source note and lowers confidence to reflect reduced evidentiary weight. This is flag-and-decay, not deletion.
• No memory-specific auto-deletion — the curator never auto-deletes an agent-session source note. Deletion of any page (including stale session memories) requires explicit editorial intent from the user, surfaced as a report-only item.

In all cases the curator uses status: stale and confidence — the canonical lifecycle fields defined in vault/CLAUDE.md — with no new field and no parallel staleness system.

Phase 3 — Auto-apply safe fixes

Execute in order. Each fix is idempotent and content-preserving.

3.1 Wrap plain-string sources: in wikilinks

For every page where sources: contains entries not in [[...]] form:

1. Read the file.
2. For each non-wikilink entry, search wiki/_sources/ for a page with matching title:.
3. If found, wrap as "[[Title]]". If not, do not wrap — surface as a report-only item.

Same rule for related, contradicts, supersedes, depends_on, scope, parent, children, child_indexes.

3.2 Fill missing parent: / path:

For every page missing parent: or path::

1. Determine the containing folder (relative to wiki/).
2. Set path: to that folder path.
3. Set parent: to the folder's folder-note title (the folder note is <folder>/<folder>.md; legacy _index.md if present), wrapped as "[[Title]]".
4. Special cases: _sources/ and _synthesis/ → parent: "" and path: "_sources" / "_synthesis". Top-level folder notes → parent: "[[Wiki Index]]".

3.3 Add title to aliases (ghost-node prevention)

For every page where title is not the first entry in aliases:

1. If aliases is missing or empty, create it with title as the first entry.
2. Otherwise prepend title. Keep all existing aliases.
3. For folder notes, also add topic-name variants (kebab-case slug, Title Case, common abbreviations).

3.4 Repair folder-note children drift

For every per-folder index — the folder note (<folder>/<folder>.md), or legacy _index.md if present:

1. List actual .md files in the folder (excluding the index note itself).
2. Add missing titles to children:.
3. Remove stale entries from children: that have no matching file.
4. Add missing body entries — children listed but not mentioned in the index body get a - [[Title]] — summary line.
5. Populate child_indexes: from subfolders that have an index note (folder note, or legacy _index.md), as quoted "[[wikilink]]" entries.

3.5 Repair wiki/index.md

1. Read every wiki page's title: and type:.
2. Add missing under the correct heading:
   • type: source → ## Sources
   • type: entity | concept → under the topic heading in ## Topics
   • type: synthesis → ## Synthesis
3. Remove stale entries with no matching file.
4. Deduplicate repeated titles.

3.6 Clean ghost wikilinks in log.md

For each [[Target]] in log.md where Target matches no real page title/alias, replace with backtick code formatting (e.g., `_index`).

3.7 Resolve broken and ghost wikilinks (safe paths only)

Always rewrite to piped basename form [[file-basename|Display]] — never to a page's bare title:. Obsidian resolves a written link by path/basename only, so a bare [[Title Case]] link relying on alias/title is itself a ghost node.

For each ghost link (a wikilink-ghost finding from the verifier §1.1b — resolves only via alias:/title:, not path/basename):

1. The finding names the file it resolves to. Rewrite the link to that file's basename in piped form, preserving the existing display text: [[Context Engineering]] → [[context-engineering|Context Engineering]].
2. If the bare target's basename is not unique vault-wide, path-qualify instead.

For each broken (dangling) [[Target]] that resolves to nothing:

1. Alias / unique-fuzzy match — if exactly one page matches Target via its aliases:, or via a case-only/hyphen-only difference, rewrite the link to that page's basename in piped form [[file-basename|Display]].
2. Anything else → leave the link, surface in the report-only list. Do not create stub pages. Do not delete the link.

3.8 Connect orphan pages (link-only, non-destructive)

For each orphan page:

1. Find the containing folder's folder note (or legacy _index.md). If the page is not in the body, add - [[file-basename|Title]] — summary (piped basename, not a bare [[Title]]).
2. For sibling pages in the same folder sharing 2+ sources, add this page to their related:.

Do NOT auto-edit sources: fields to connect type: source orphans. Mutating sources: forges a provenance claim the user never made and is the exact drift SECURITY.md calls out. Surface every unlinked type: source orphan as a Report-only item with candidate pages suggested in the report (most relevant concept/entity pages found by grep over body text + shared entities). The user — not this agent — decides whether the source actually backs the target page.

Never delete an orphan. Unresolvable orphans stay as report-only items.

3.9 Add missing graph color groups

For each top-level topic folder without a matching path:wiki/<folder> color group:

1. Read current groups via obsidian eval.
2. Pick the next unused palette color per /claude-wiki-pages:obsidian-graph-colors.
3. Insert before the _sources / _synthesis special groups (there is no index catch-all — folder notes take their topic's color; never add groups for raw/, _templates/, or _proposed/ — those paths are excluded from Obsidian's index).
4. Apply via obsidian eval + graph.saveOptions().

Phase 4 — Judgment fixes (automatic, under the checkpoint)

Judgment fixes apply automatically — there is no approval prompt. The preflight engine.sh heal already wrote a git checkpoint, so every change here is reversible with git revert <healCommit>. Record what you do in a heal log at vault/output/_heal-log-YYYY-MM-DD.md (a record, not a request):

# Lint plan — YYYY-MM-DD

## Flat folders to restructure (WARN: >12 children)
<folder-a>/ (18 pages) → proposed:
  <folder-a>/subtopic-x/  (<n> pages: <list>)
  <folder-a>/subtopic-y/  (<n> pages: <list>)

## Title collisions to resolve (ERROR)
- "<Title>" appears in: <file-a>, <file-b>
  Proposal: rename <file-b> to "<Title> (Context)"

## Body wikilinks to densify (INFO, opt-in)
- N mentions across M pages

## Mergeable near-duplicates (INFO, opt-in)
- <page-a> and <page-b> (Jaccard ≥ 0.6) — canonical: <page-a>

## Summary
- git mv: N
- frontmatter rewrites: N
- body edits: N

Then execute the changes directly:

1. Backlink-safe rename first (renames and moves). For each rename or move, try bash ${CLAUDE_PLUGIN_ROOT}/scripts/obsidian-rename.sh --target <vault> --from <old-rel.md> --to <new-rel.md>.
   • Exit 0 — Obsidian performed the rename and updated every [[wikilink]] backlink from its metadata cache: skip the manual body-wikilink rewrite for that page (title-collision renames especially — that is the error-prone rewrite this path eliminates). Note: the CLI write bypasses the PreToolUse hooks, which is why the Phase 5 re-verify below is mandatory, not optional.
   • Exit 3 ([skip] cli-rename: obsidian-cli unavailable) — fall back to the manual sequence: git mv, then for a rename also rewrite the old [[Title]] body wikilinks across pages (folder moves don't break title-based wikilinks).
   • Exit 2 — argument error; fix the paths, do not fall back blindly.
2. Frontmatter and indexes (both branches — Obsidian does not know our schema). Update parent:/path: on every moved page. Update the parent folder note (children: / child_indexes:). Update wiki/index.md.

After executing, re-run engine.sh verify --json; if errors remain, iterate once more, then surface any residual that genuinely needs editorial intent (deletions, ambiguous merges) for the user — do not guess at intent.

Tell the user where the rollback point is:

Applied N judgment fixes (restructures, merges, densification) automatically.
Reversible: git revert <healCommit>   (or: git checkout <checkpoint>)
Heal log: vault/output/_heal-log-YYYY-MM-DD.md

Phase 6 — Report template

Print this report (the agent body summarizes the section list):

## Lint & Fix report

### Diagnosis
- Errors: N   Warnings: N   Info: N

### Classification
- Repaired by engine: N
- Auto-applied: N
- Judgment fixes applied: N
- Surfaced for review: N

### Auto-fixes applied
- sources fields wrapped: N
- parent/path filled: N
- titles added to aliases: N
- folder-note children repaired: N
- wiki/index.md repaired: N
- ghost wikilinks in log.md cleaned: N
- broken wikilinks auto-resolved: N
- orphans connected: N
- graph color groups added: N

### Judgment fixes applied (automatic, under checkpoint)
<list with before/after>

### Surfaced for review (editorial intent required)
<list each item with file path>

### Verification
- engine verify errors: before N → after N
- engine verify warnings: before N → after N
- Rollback: git revert <healCommit>  ·  Heal log: vault/output/_heal-log-YYYY-MM-DD.md