Wiki Lint — Health Audit

You are performing a health check on an Obsidian wiki. Your goal is to find and fix structural issues that degrade the wiki's value over time.

Before scanning anything: follow the Retrieval Primitives table in llm-wiki/SKILL.md. Prefer frontmatter-scoped greps and section-anchored reads over full-page reads. On a large vault, blindly reading every page to lint it is exactly what this framework is built to avoid.

Flat-Vault Variant (optional)

Some vaults use a single notes/ folder instead of category folders, expressing the category via frontmatter (category: concept|entity|reference|insight). The starter vault shipped with this kit works this way. When the vault is flat, apply these overrides before running any checks:

When flat, all notes live in notes/ only. Categories are expressed via frontmatter category: concept|entity|reference|insight, not via folders.

Also verify after every lint run: are _system/index.md and _system/hot.md up to date? If notes exist in notes/ that are missing from index.md, flag and offer to add them.

Synthesis Gap behavior (trigger 3 of 3): When check #11 finds synthesis gaps, do NOT list all of them. Instead:

1. Rank gaps by co-occurrence count (highest first)
2. Pick only the top 1
3. After the full lint report, ask the user one question:

"[[notes/X]] and [[notes/Y]] co-occur N times but have no insight page connecting them — want me to draft one now?"

• If yes → create the insight note using the template in wiki-query/SKILL.md, then update index.md and hot.md
• If no → drop it completely, no todo created
• Never offer more than one synthesis at a time

Before You Start

1. Resolve the vault path (precedence, highest first): the OBSIDIAN_VAULT_PATH environment variable if set, else a .env in the current working directory (vault-scoped), else ~/.obsidian-wiki/config (global default).
2. Read index.md for the full page inventory
3. Read log.md for recent activity context

Lint Checks

Run these checks in order. Report findings as you go.

1. Orphaned Pages

Find pages with zero incoming wikilinks. These are knowledge islands that nothing connects to.

How to check:

• Glob all .md files in the vault
• For each page, Grep the rest of the vault for [[page-name]] references
• Pages with zero incoming links (except index.md and log.md) are orphans

How to fix:

• Identify which existing pages should link to the orphan
• Add wikilinks in appropriate sections

2. Broken Wikilinks

Find [[wikilinks]] that point to pages that don't exist.

How to check:

• Grep for \[\[.*?\]\] across all pages
• Extract the link targets
• Check if a corresponding .md file exists

How to fix:

• If the target was renamed, update the link
• If the target should exist, create it
• If the link is wrong, remove or correct it

3. Missing Frontmatter

Every page should have: title, category, tags, sources, created, updated.

How to check:

• Grep frontmatter blocks (scope to ^--- at file heads) instead of reading every page in full
• Flag pages missing required fields

How to fix:

• Add missing fields with reasonable defaults

3a. Missing Summary (soft warning)

Every page should have a summary: frontmatter field — 1–2 sentences, ≤200 chars. This is what cheap retrieval (e.g. wiki-query's index-only mode) reads to avoid opening page bodies.

How to check:

• Grep frontmatter for ^summary: across the vault
• Flag pages without it, but as a soft warning, not an error — older pages predating this field are fine; the check exists to nudge ingest skills into filling it on new writes.
• Also flag pages whose summary exceeds 200 chars.

How to fix:

• Re-ingest the page, or manually write a short summary (1–2 sentences of the page's content).

4. Stale Content

Pages whose updated timestamp is old relative to their sources.

How to check:

• Compare page updated timestamps to source file modification times
• Flag pages where sources have been modified after the page was last updated

5. Contradictions

Claims that conflict across pages.

How to check:

• This requires reading related pages and comparing claims
• Focus on pages that share tags or are heavily cross-referenced
• Look for phrases like "however", "in contrast", "despite" that may signal existing acknowledged contradictions vs. unacknowledged ones

How to fix:

• Add an "Open Questions" section noting the contradiction
• Reference both sources and their claims

6. Index Consistency

Verify index.md matches the actual page inventory.

How to check:

• Compare pages listed in index.md to actual files on disk
• Check that summaries in index.md still match page content

7. Provenance Drift

Check whether pages are being honest about how much of their content is inferred vs extracted. See the Provenance Markers section in llm-wiki for the convention.

How to check:

• For each page with a provenance: block or any ^[inferred]/^[ambiguous] markers, count sentences/bullets and how many end with each marker
• Compute rough fractions (extracted, inferred, ambiguous)
• Apply these thresholds:
  • AMBIGUOUS > 15%: flag as "speculation-heavy" — even 1-in-7 claims being genuinely uncertain is a signal the page needs tighter sourcing or should be moved to synthesis/
  • INFERRED > 40% with no sources: in frontmatter: flag as "unsourced synthesis" — the page is making connections but has nothing to cite
  • Hub pages (top 10 by incoming wikilink count) with INFERRED > 20%: flag as "high-traffic page with questionable provenance" — errors on hub pages propagate to every page that links to them
  • Drift: if the page has a provenance: frontmatter block, flag it when any field is more than 0.20 off from the recomputed value
• Skip pages with no provenance: frontmatter and no markers — treated as fully extracted by convention

How to fix:

• For ambiguous-heavy: re-ingest from sources, resolve the uncertain claims, or split speculative content into a synthesis/ page
• For unsourced synthesis: add sources: to frontmatter or clearly label the page as synthesis
• For hub pages with INFERRED > 20%: prioritize for re-ingestion — errors here have the widest blast radius
• For drift: update the provenance: frontmatter to match the recomputed values

8. Fragmented Tag Clusters

Checks whether pages that share a tag are actually linked to each other. Tags imply a topic cluster; if those pages don't reference each other, the cluster is fragmented — knowledge islands that should be woven together.

How to check:

• For each tag that appears on ≥ 5 pages:
  • n = count of pages with this tag
  • actual_links = count of wikilinks between any two pages in this tag group (check both directions)
  • cohesion = actual_links / (n × (n−1) / 2)
• Flag any tag group where cohesion < 0.15 and n ≥ 5

How to fix:

• Run the cross-linker skill targeted at the fragmented tag — it will surface and insert the missing links
• If a tag group is large (n > 15) and still fragmented, consider splitting it into more specific sub-tags

9. Visibility Tag Consistency

Checks that visibility/ tags are applied correctly and aren't silently missing where they matter.

How to check:

• Untagged PII patterns: Grep page bodies for patterns that commonly indicate sensitive data — lines containing password, api_key, secret, token, ssn, email:, phone: followed by an actual value (not a field description). If a page matches and lacks visibility/pii or visibility/internal, flag it as a likely mis-classification.
• visibility/pii without sources:: A page tagged visibility/pii should always have a sources: frontmatter field — if there's no provenance, there's no way to verify the classification. Flag any visibility/pii page missing sources:.
• Visibility tags in taxonomy: visibility/ tags are system tags and must not appear in _meta/taxonomy.md. If found there, flag as misconfigured — they'd be counted toward the 5-tag limit on pages that include them.

How to fix:

• For untagged PII patterns: add visibility/pii (or visibility/internal if it's team-context rather than personal data) to the page's frontmatter tags
• For missing sources:: add provenance or escalate to the user — don't auto-fill
• For taxonomy contamination: remove the visibility/ entries from _meta/taxonomy.md

10. Misc Promotion Candidates

Find pages in misc/ that have accumulated enough project affinity to be promoted.

How to check:

• Glob $OBSIDIAN_VAULT_PATH/misc/*.md
• For each page, read the affinity frontmatter field
• Flag pages where any single project's score ≥ 3

How to fix:

• Run the cross-linker skill first if affinity scores look stale (e.g., affinity: {} on a page with many wikilinks)
• To promote: move the page to projects/<project-name>/references/ (or another appropriate category), update its category frontmatter, remove promotion_status, and grep the vault for backlinks to update them

11. Synthesis Gaps

Identify high-value synthesis opportunities the wiki is missing — concept pairs that co-occur across many pages but have no synthesis/ page connecting them.

How to check:

• List all pages in synthesis/ — collect the concept pairs each one already covers (from its [[wikilinks]] or title)
• Pick 10-15 frequently linked concepts from concepts/ and entities/
• For each pair, run a quick grep to count pages that link to both:

  grep -rl "\[\[ConceptA\]\]" "$OBSIDIAN_VAULT_PATH" --include="*.md" > /tmp/a.txt
  grep -rl "\[\[ConceptB\]\]" "$OBSIDIAN_VAULT_PATH" --include="*.md" > /tmp/b.txt
  comm -12 <(sort /tmp/a.txt) <(sort /tmp/b.txt) | wc -l

• Flag pairs with co-occurrence ≥ 3 that have no existing synthesis page

How to fix:

• Run /wiki-synthesize to automatically discover and fill the top gaps

Output Format

Report findings as a structured list:

## Wiki Health Report

### Orphaned Pages (N found)
- `concepts/foo.md` — no incoming links

### Broken Wikilinks (N found)
- `entities/bar.md:15` — links to [[nonexistent-page]]

### Missing Frontmatter (N found)
- `skills/baz.md` — missing: tags, sources

### Stale Content (N found)
- `references/paper-x.md` — source modified 2024-03-10, page last updated 2024-01-05

### Contradictions (N found)
- `concepts/scaling.md` claims "X" but `synthesis/efficiency.md` claims "not X"

### Index Issues (N found)
- `concepts/new-page.md` exists on disk but not in index.md

### Missing Summary (N found — soft)
- `concepts/foo.md` — no `summary:` field
- `entities/bar.md` — summary exceeds 200 chars

### Provenance Issues (N found)
- `concepts/scaling.md` — AMBIGUOUS > 15%: 22% of claims are ambiguous (re-source or move to synthesis/)
- `entities/some-tool.md` — drift: frontmatter says inferred=0.10, recomputed=0.45
- `concepts/transformers.md` — hub page (31 incoming links) with INFERRED=28%: errors here propagate widely
- `synthesis/speculation.md` — unsourced synthesis: no `sources:` field, 55% inferred

### Fragmented Tag Clusters (N found)
- **#systems** — 7 pages, cohesion=0.06 ⚠️ — run cross-linker on this tag
- **#databases** — 5 pages, cohesion=0.10 ⚠️

### Visibility Issues (N found)
- `entities/user-records.md` — contains `email:` value pattern but no `visibility/pii` tag
- `concepts/auth-flow.md` — tagged `visibility/pii` but missing `sources:` frontmatter
- `_meta/taxonomy.md` — contains `visibility/internal` entry (system tag must not be in taxonomy)

### Misc Promotion Candidates (N found)
Pages in misc/ that have ≥ 3 connections to a single project and are ready to be promoted:

| Page | Top Project | Affinity Score |
|---|---|---|
| `misc/web-martinfowler-articles-microservices.md` | `obsidian-wiki` | 4 |

### Synthesis Gaps (N found)
Concept pairs that co-occur frequently but have no synthesis page:

| Pair | Co-occurrence | Suggested Action |
|---|---|---|
| [[Caching]] × [[Consistency]] | 5 pages | Run `/wiki-synthesize` |
| [[Testing]] × [[Observability]] | 3 pages | Run `/wiki-synthesize` |

After Linting

Append to log.md:

- [TIMESTAMP] LINT issues_found=N orphans=X broken_links=Y stale=Z contradictions=W prov_issues=P missing_summary=S fragmented_clusters=F visibility_issues=V promotion_candidates=C synthesis_gaps=G

Offer to fix issues automatically or let the user decide which to address.