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.

Before You Start

Writing profile: Before drafting or rewriting natural-language Markdown, read and apply the Writing Profile Resolution section in llm-wiki/SKILL.md. Framework schema, provenance, safety, and operation-specific requirements take precedence. Apply WRITING.md preferences only to generated consolidation reports; deterministic findings and fixes keep their existing formats.

1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → global config → prompt setup). This gives OBSIDIAN_VAULT_PATH plus any OBSIDIAN_ALLOWED_LIFECYCLES, OBSIDIAN_ALLOWED_RELATIONSHIP_TYPES, OBSIDIAN_REQUIRED_TRUST_FIELDS, and OBSIDIAN_SCHEMA_SOURCE values.
2. Read owner rules — if $OBSIDIAN_VAULT_PATH/AGENTS.md exists, read it before interpreting any schema. Owner rules override framework defaults.
3. Form the effective schema — record the schema source locator plus effective required/optional frontmatter, lifecycle values, relationship types, and provenance markers. Framework values are defaults; preserve owner extensions and relaxed requiredness exactly. Never coerce an owner type to a framework type.
4. Read index.md for the full page inventory
5. Read log.md for recent activity context

Pass the effective schema to deterministic checks explicitly. For example, add each owner extension with --allow-lifecycle / --allow-relationship-type, replace trust requiredness with repeatable --required-trust-field, and identify the authority with --schema-source "$OBSIDIAN_VAULT_PATH/AGENTS.md". The JSON report's schema block must match the schema you formed before findings are accepted.

Schema precedence is CLI flags > resolved environment/config values > framework defaults; lifecycle and relationship extensions remain additive. Strip every override before use. An explicitly configured empty or whitespace-only value—and any empty comma-separated list entry—fails closed; never treat it as a valid lifecycle, relationship type, required field, or authority locator. Remove the variable instead when defaults are intended.

When obsidian-wiki is on PATH, prefer obsidian-wiki lint "$OBSIDIAN_VAULT_PATH" --json (with the same schema override flags as above) and fold the JSON findings into the health report. If the CLI is unavailable, keep the grep-based checks below — do not require the binary.

If the JSON report includes findings.snapshot_mismatch, list those pages in the report. Missing or drifted snapshots: is not missing required frontmatter (section 3 still covers only title, category, tags, sources, created, updated). Do not rewrite sources: to fix snapshot drift. Run obsidian-wiki snapshots apply --from-json <lint.json> (dry-run), show the preview, and pass --apply only after explicit user confirmation. Apply writes quoted "[[_raw/_archived/stem|stem]]" list items (native Property links with display text). wiki-lint --consolidate still does not apply this finding.

Lint Checks

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

Scope: skip _archives/, _raw/, _readouts/, and .obsidian/ in every check. These hold frozen snapshots, unprocessed staging drafts, and derived readouts (saved by wiki-narrate) — they are not knowledge-graph pages, so orphan, frontmatter, and link checks don't apply to them.

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 target: drop everything from the first | (alias) or # (heading/block anchor), and strip a trailing backslash left by an escaped \| inside a table cell
• Skip a target whose extension is an attachment type (.png, .jpg, .gif, .svg, .webp, .pdf, .canvas, .base, audio and video): it's an embed, not a page link, and has no entry in the .md inventory this check compares against
• Do not treat every dot as an extension — [[Node.js]], [[Next.js]], and [[v1.2 release notes]] are page links whose names happen to contain a dot, and dropping them would both miss real broken links and make the target page look like an orphan
• Strip an explicit .md suffix from what remains, then 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

Uncovered sources. obsidian-wiki lint reports uncovered_sources: .manifest.json entries whose pages_produced/pages_created/pages_updated list is empty (no_pages) or names only pages that no longer exist (pages_missing). Each one is a source the vault says it ingested but no page now carries. A warning. For each, re-ingest the source, or point the manifest entry at the page that absorbed it (after a rename or wiki-dedup merge). Never delete the entry to silence the finding.

Undated claims (line-level). obsidian-wiki lint reports undated_claims: lines stating a count or amount that goes stale (stars, users, customers, downloads, deals, MRR/ARR) with no date on the line. Lines under a dated heading, pages in journal/ or named YYYY-MM-…, code, and blockquotes are exempt. A warning, never a failure. For each one, either re-check the number and stamp it (as of YYYY-MM-DD), replace it with a link to where the live number lives, or move it under a dated heading as history.

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

12. Confidence and Lifecycle Schema

Enforces the confidence + lifecycle frontmatter schema (see llm-wiki/SKILL.md, Confidence and Lifecycle section).

Two modes:

• --check (default, read-only) — reports errors and warnings
• --consolidate — may apply separately approved structural maintenance, but never rewrites base_confidence

Confidence is a semantic judgment. A deterministic tool cannot infer independent evidence lineages or whole-page claim coverage from source strings alone. Confidence automation therefore validates an explicitly approved manual trust ledger; it never substitutes URL counting for review.

Rule 12a — lifecycle enum validation

How to check: Grep frontmatter for ^lifecycle: across all pages. Flag any value outside the effective lifecycle set (framework default: {draft, reviewed, verified, disputed, archived}).

How to fix: n/a (only a human should set lifecycle state)

Rule 12b — base_confidence range

How to check: Grep frontmatter for ^base_confidence: across all pages. Flag any present value outside [0.0, 1.0]; flag absence only when the effective owner schema requires the field.

How to fix: n/a (wrong value means the skill computed it wrong — surface for manual correction)

Rule 12c — Stale page report (computed overlay)

Staleness is never stored — it is computed at read time: is_stale = (today − updated) > 90 days.

How to check: For each page, read updated: from frontmatter and compute is_stale. If stale, also check lifecycle:. Report:

• Stale pages with lifecycle: verified with a louder annotation (these are the most dangerous — high-trust pages that may be wrong)
• All other stale pages as a standard warning

How to fix: --fix does not rewrite lifecycle. Staleness clears automatically when a re-ingest bumps updated.

Rule 12c-2 — Illegal lifecycle transitions

The lifecycle enum is a state machine, not a free-form label. obsidian-wiki lint reports illegal_lifecycle_transitions by comparing each page's current lifecycle against the value recorded in _meta/trust-ledger.json at its last review.

Flagged: any state falling back to draft (only ingest sets draft), and any exit from archived (terminal — a restore is a deliberate human delete-and-recreate).

Not flagged: draft → verified. Ledger snapshots are sparse, so a legitimate intermediate reviewed may have happened between two reviews; flagging it would fire on valid history.

Warns by default; fails under --strict-trust. Pages whose ledger entry predates the lifecycle field have no baseline and are skipped silently.

How to fix: n/a — a page that moved along a forbidden edge means either a skill wrote lifecycle when it shouldn't have, or a human transition needs recording. Surface for human resolution.

Rule 12d — Supersession integrity

How to check: For each page with superseded_by: "[[target]]":

• Verify the target page exists
• Verify the target page is not itself archived (no circular or chained supersession)
• Verify there are no cycles (A supersedes B which supersedes A)
• Warn if lifecycle != archived while superseded_by is set (inconsistent state)

How to fix: n/a — flag for human resolution

Rule 12e — Confidence review integrity

How to check: Run the deterministic ledger validator first:

obsidian-wiki trust-check "$OBSIDIAN_VAULT_PATH" --strict --json --pretty

Use --strict for CI and scheduled gates: stale, unreviewed, or missing-page warnings then return nonzero. Without --strict, trust-check remains a read-only reporting command and returns nonzero only for hard ledger errors or score mismatches.

The approved ledger lives at _meta/trust-ledger.json. Each entry records the human-reviewed score plus a SHA-256 fingerprint of material page content and evidence metadata. The fingerprint excludes volatile bookkeeping (updated, base_confidence, and lifecycle transition fields), so timestamp-only edits do not reopen review.

Interpret results as follows:

• reviewed — current material fingerprint and stored score both match the approved review; do not recompute from source strings.
• stale — body, summary, sources, provenance, tags, or relationships changed; perform a new manual lineage + claim-coverage review.
• unreviewed — page has no approved ledger entry; manual review is required.
• ignored_entries — how many reviewed pages are now excluded by .okignore. A count only, so the pages stay unnamed. Any trust-record clears them.
• score_mismatches — material content still matches, but stored base_confidence differs from the approved value; fail the lint.
• errors — malformed/missing ledger data; fail the lint.

For a separately approved full-vault review, record the accepted state explicitly:

obsidian-wiki trust-record "$OBSIDIAN_VAULT_PATH" \
  --all --reviewed-at "<ISO-8601 timestamp>" --approved --json --pretty

After a separately approved review of only specific stale/unreviewed pages, update only those entries:

obsidian-wiki trust-record "$OBSIDIAN_VAULT_PATH" \
  --page "concepts/example.md" --page "skills/example.md" \
  --reviewed-at "<ISO-8601 timestamp>" --approved --json --pretty

--approved means a human approved every score being recorded. It is a workflow assertion, not a cryptographic signature: keep _meta/trust-ledger.json under version control and require human diff review before merging ledger changes. --all is valid only after a full-vault review; use repeatable --page for partial reviews so unrelated stale pages remain open. Never run trust-record merely to silence warnings.

Manual recomputation protocol for stale/unreviewed pages:

1. Decompose the page into material claims and map each claim to evidence.
2. Collapse dependent evidence into independent lineages: files/commits from one repository, retries in one task chain, snapshots plus their captured source, duplicate memories, and parent/child tasks each count once.
3. Assign reviewed quality per independent lineage using llm-wiki buckets.
4. Compute the raw base score, then assess whole-page claim coverage. The formula is a starting point, not an automatic target.
5. Classify the result as raise, keep, lower, or repair first; require approval before changing base_confidence or refreshing the ledger.

How to fix: There is no automatic confidence fix. Apply only an explicitly approved exact patch, verify its scope, then refresh only the reviewed ledger state. --consolidate must never rewrite base_confidence.

Current enforcement

Under framework defaults, every non-reserved content page must contain a finite base_confidence in [0.0, 1.0] and a documented lifecycle value. An owner schema may relax either field; present values remain validated. Missing or malformed trust fields, malformed ledger data, and a missing required ledger are hard errors. New pages with valid trust fields but no approved ledger entry are unreviewed; material changes to approved pages are stale.

Output additions

Add to the Wiki Health Report:

### Confidence/Lifecycle Issues (N found)
- `concepts/foo.md` — missing `lifecycle` field (warning: Phase 1)
- `entities/bar.md` — `lifecycle: stalestate` is not a valid enum value
- `concepts/scaling.md` — `base_confidence: 1.4` is out of range [0.0, 1.0]
- `synthesis/old-analysis.md` — STALE (last updated 2025-10-01, 182 days ago) lifecycle=verified ⚠️ HIGH PRIORITY
- `concepts/outdated.md` — STALE (last updated 2025-11-15, 137 days ago) lifecycle=draft
- `entities/tool-v1.md` — `superseded_by: [[entities/tool-v2]]` but lifecycle=draft (expected archived)
- `concepts/drift-example.md` — confidence review stale: material fingerprint changed; manual lineage + coverage review required
- `entities/mismatch.md` — confidence mismatch: stored=0.80, approved=0.59

Append to the LINT log entry:

- [TIMESTAMP] LINT ... lifecycle_issues=N

13. Typed Relationships Validity

Validate relationships: frontmatter blocks. Skip pages that have no relationships: block — the field is optional.

Framework-default types: extends, implements, contradicts, derived_from, uses, replaces, related_to. Validate against the effective set after applying owner extensions.

How to check:

• Grep frontmatter for ^relationships: across all vault pages
• For each page that has a relationships: block, read its frontmatter (not the full page body)
• For each entry in the block:
  1. Type validation — flag any type: value not in the allowed set above
  2. Broken target — strip [[ and ]] from the target: string, normalize (lowercase, spaces→hyphens, strip .md), and check whether a .md file at that path exists in the vault. Flag unresolved targets. Before normalizing, drop everything from the first | (alias) or # (heading/block anchor): a pipe-aliased or heading-anchored target is not broken just because the literal bracket contents don't match a filename.
  3. Self-reference — flag any entry where the resolved target equals the page's own node id

How to fix:

• Invalid type: report the value and effective schema source. Correct it only if it is absent from both framework defaults and owner extensions; never replace a valid owner type with related_to.
• Broken target: update or remove the entry; if the target page should exist, create it first
• Self-reference: remove the entry

Output additions:

### Typed Relationship Issues (N found)
- `concepts/foo.md` — relationships[1]: type "contradication" is not an allowed type (did you mean "contradicts"?)
- `concepts/bar.md` — relationships[0]: target "[[skills/nonexistent-skill]]" resolves to no page in vault
- `entities/baz.md` — relationships[2]: self-reference (target resolves to this page's own id)

Append to the LINT log entry:

... relationship_issues=N

14. Event-Time Validity

Validate valid_from / valid_until / superseded_by frontmatter. All three are optional — skip pages that carry none of them.

created/updated are ingestion time; these three are event time, when the claim itself was true. A page whose valid_until has passed is historical, not wrong: it stays in the vault and in the graph, and only drops out of default retrieval.

How to check:

• Grep frontmatter for ^valid_from:, ^valid_until:, ^superseded_by: across all vault pages
• For each page that has any of them:
  1. Date parseability — each value must be YYYY-MM-DD or a full ISO 8601 timestamp. Flag anything else.
  2. Window order — flag any page where valid_until precedes valid_from
  3. Dangling successor — strip [[/]] from superseded_by, drop everything from the first | or #, strip .md, normalize, and check the page exists. Flag unresolved targets and self-references.

obsidian-wiki lint reports all three as temporal_errors (dates, windows) and superseded_dangling (successors). A bracketed dangling successor also shows up in broken_links.

Why the dates fail rather than warn: retrieval treats an unparseable window as current, so an unreported typo lets a stale claim answer as fact — the exact failure the fields exist to prevent.

How to fix:

• Unparseable date: rewrite as YYYY-MM-DD; if the real date is unknown, remove the field rather than guessing
• Inverted window: confirm which date is wrong with the page's sources; never silently swap them
• Dangling successor: create the replacement page, correct the pointer, or remove it if nothing replaced the claim
• Never "fix" a historical page by rewriting it as current — that destroys the record the window exists to keep

Output additions:

### Event-Time Issues (N found)
- `references/gateway-nginx.md` — valid_until (2026-04-01) precedes valid_from (2026-05-01)
- `references/old-limits.md` — valid_until "soon" is not a date
- `references/legacy-auth.md` — superseded_by "[[oauth-rollout]]" resolves to no page in vault

Append to the LINT log entry:

... temporal_issues=N

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:

  rg -l --glob '*.md' "\[\[ConceptA\]\]" "$OBSIDIAN_VAULT_PATH" > /tmp/a.txt
  rg -l --glob '*.md' "\[\[ConceptB\]\]" "$OBSIDIAN_VAULT_PATH" > /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
- `projects/foo.md:28` — undated claim: "GitHub: 6★" (stamp it, link it, or date the heading)

### 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 |

### Typed Relationship Issues (N found)
- `concepts/foo.md` — relationships[1]: type "contradication" is not an allowed type
- `concepts/bar.md` — relationships[0]: target "[[skills/nonexistent]]" resolves to no page

### 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 relationship_issues=R

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

Consolidate Mode (--consolidate)

Triggered by wiki-lint --consolidate. Switches from report-only to act-and-report — the "dream cycle" that runs periodically so the wiki self-heals.

Safety protocol

Always run in dry-run first. Before writing anything:

1. Run all 12 lint checks (Step 1–12 above).
2. Print the planned consolidation actions as a structured list (see Dry-Run Output below).
3. Ask the user: "Apply these N changes? [yes / no / select]".
4. Only proceed with writes after explicit confirmation. If the user selects individual actions, apply only those.
5. Never merge pages — use wiki-dedup for that. Only link, promote, demote, and flag. Never apply snapshot_mismatch here; that stays on the snapshots CLI with its own confirmation (see Before You Start).

Consolidation actions (in order, after confirmation)

Pre-write snapshot — before the first file write, check whether the vault itself is the root of a Git repository. Merely being a subdirectory of a larger repository does not qualify: running git add -A there could capture unrelated files. If the vault is not a standalone Git repository, skip this step silently — no nagging, no suggesting git init.

VAULT_REAL_PATH=$(cd "$OBSIDIAN_VAULT_PATH" && pwd -P)
VAULT_GIT_ROOT=$(git -C "$OBSIDIAN_VAULT_PATH" rev-parse --show-toplevel 2>/dev/null || true)
SNAPSHOT_SHA=""

if [ -n "$VAULT_GIT_ROOT" ] && [ "$VAULT_GIT_ROOT" = "$VAULT_REAL_PATH" ]; then
  if git -C "$OBSIDIAN_VAULT_PATH" diff --quiet \
    && git -C "$OBSIDIAN_VAULT_PATH" diff --cached --quiet \
    && [ -z "$(git -C "$OBSIDIAN_VAULT_PATH" ls-files --others --exclude-standard)" ]; then
    SNAPSHOT_SHA=$(git -C "$OBSIDIAN_VAULT_PATH" rev-parse HEAD)
  else
    if ! git -C "$OBSIDIAN_VAULT_PATH" add -A; then
      echo "Pre-write snapshot failed; abort the skill without writing any vault files." >&2
      exit 1
    fi
    if ! git -C "$OBSIDIAN_VAULT_PATH" commit -m "pre-wiki-lint snapshot" --quiet; then
      echo "Pre-write snapshot failed; abort the skill without writing any vault files." >&2
      exit 1
    fi
    SNAPSHOT_SHA=$(git -C "$OBSIDIAN_VAULT_PATH" rev-parse HEAD)
  fi
fi

The clean-repository branch deliberately avoids calling git commit, so "nothing to commit" is not treated as an error. If git add or git commit fails, stop before editing the vault; never continue without the promised snapshot.

If SNAPSHOT_SHA is non-empty and the skill writes files, include the SHA in the final report. To discard the entire run, after confirming there are no later changes worth keeping, the user can run:

git -C "$OBSIDIAN_VAULT_PATH" reset --hard "$SNAPSHOT_SHA"
git -C "$OBSIDIAN_VAULT_PATH" clean -fd

Action 1: Fix broken wikilinks

For each broken [[Target]] found in Check 2:

• Search the vault for a page whose title or filename is the closest fuzzy match (use Grep across index.md titles)
• If a unique best match exists (edit distance ≤ 2 characters or same root word): rewrite the link. Note the rewrite: [[Oringal]] → [[corrected-page]].
• If no match or ambiguous: convert to plain text (~~[[Target]]~~ → Target) and add a comment <!-- broken link: no match found -->.
• Never create a new page just to satisfy a broken link.

Action 2: Add missing cross-references for orphans

For each orphan page found in Check 1 (zero incoming links):

• Grep the vault body text for mentions of the page's title or aliases (case-insensitive).
• For each mention found in another page, add a [[wikilink]] replacing the plain-text mention.
• Limit to 3 insertions per orphan — don't flood pages with links.
• This is scoped to orphans only (different from cross-linker which runs broadly).

Action 3: Correct lifecycle states

Apply these rules automatically (they don't require human judgment — they enforce the documented state machine):

• Promote draft → reviewed: pages where lifecycle: draft AND created > 30 days ago AND base_confidence > 0.7. Set lifecycle: reviewed, lifecycle_changed: <today>, lifecycle_reason: "auto-promoted by wiki-lint --consolidate: age>30d, confidence>0.7".
• Demote verified → stale: NOT a state transition — stale is a computed overlay, not a lifecycle value. Instead: for verified pages where is_stale = (today − updated) > 180 days, add a callout at the top of the page body: > ⚠️ **Stale**: This page was last updated <date>. Verify before relying on it. Only add if the callout isn't already present.
• Do not change reviewed → verified or any other transition — those are human-only.

Action 4: Tier demotion

For pages with tier: supporting (or unset) that have 0 incoming links AND haven't been updated in 90+ days:

• Set tier: peripheral.
• Emit a list of demotions for the user to review.
• Do not demote tier: core pages automatically — those were manually set.

Action 5: Tag normalization

Read _meta/taxonomy.md for the alias mapping (e.g., ml → machine-learning). For each page, replace known alias tags with their canonical form in the tags: frontmatter field. This is a subset of tag-taxonomy's work — only alias fixes, no full audit.

Action 6: Contradiction callouts

For each pair of pages marked as contradicting each other (via relationships: contradicts in frontmatter, or flagged in Check 5):

• Check whether a > ⚠️ Contradiction flagged with [[Other Page]] callout already exists near the relevant claim.
• If not, add it at the end of the "Key Ideas" section (or before "Open Questions" if no "Key Ideas" section). Keep it concise — one line.
• Do not resolve the contradiction; only flag it visually.

Action 7: Write consolidation report

After all actions, write a report to synthesis/consolidation-<YYYY-MM-DD>.md:

---
title: Consolidation Report <YYYY-MM-DD>
category: synthesis
tags: [maintenance, consolidation]
sources: []
summary: Auto-generated consolidation report from wiki-lint --consolidate run on <date>.
lifecycle: draft
lifecycle_changed: <date>
tier: peripheral
created: <obsidian-wiki memory now>
updated: <obsidian-wiki memory now>
---

# Consolidation Report — <YYYY-MM-DD>

## Summary
- Broken links fixed: N
- Cross-references added: M
- Lifecycle states updated: K
- Tier demotions: D
- Tags normalized: T
- Contradiction callouts added: C

## Broken Link Fixes
- `concepts/foo.md:12` — [[OldTarget]] → [[correct-target]]
- `entities/bar.md:8` — [[Missing]] → `Missing` (no match found)

## Cross-References Added (orphan rescue)
- `concepts/baz.md` — now linked from: [[concepts/alpha]], [[skills/beta]]

## Lifecycle Updates
- `concepts/old-draft.md` — draft → reviewed (age 45d, confidence 0.74)
- `synthesis/stale-verified.md` — stale callout added (last updated 2025-10-01)

## Tier Demotions
- `concepts/unused-concept.md` — supporting → peripheral (0 links, 120 days stale)

## Tag Normalizations
- `entities/some-tool.md` — `ml` → `machine-learning`

## Contradiction Callouts
- `concepts/scaling.md` — flagged contradiction with [[synthesis/efficiency]]

Dry-Run Output (shown before any writes)

wiki-lint --consolidate — Dry Run

Planned actions (N total):
[1] Fix broken link: concepts/foo.md:12 [[OldTarget]] → [[correct-target]]
[2] Add cross-ref: concepts/baz.md ← [[concepts/alpha]] (orphan rescue)
[3] Lifecycle: concepts/old-draft.md → reviewed (age 45d, confidence 0.74)
[4] Tier demotion: concepts/unused.md → peripheral (0 links, 112 days stale)
[5] Tag alias: entities/some-tool.md: ml → machine-learning
[6] Contradiction callout: concepts/scaling.md ↔ [[synthesis/efficiency]]

Apply these 6 changes? [yes / no / select by number]

Log entry for consolidate mode

- [TIMESTAMP] LINT_CONSOLIDATE links_fixed=N orphans_rescued=M lifecycle_updates=K tier_demotions=D tag_fixes=T contradiction_callouts=C report=synthesis/consolidation-YYYY-MM-DD.md

QMD Refresh After Vault Writes

QMD is a search index, not the source of truth. If $QMD_WIKI_COLLECTION is empty or unset, skip this step. Run it only after this skill has written or rewritten vault markdown. If QMD refresh fails, do not roll back the vault changes; report the QMD status separately.

Use $QMD_CLI if set; otherwise use qmd.

${QMD_CLI:-qmd} update

If the output says vectors are needed or embeddings may be stale, run:

${QMD_CLI:-qmd} embed

Verify the collection with either:

${QMD_CLI:-qmd} ls "$QMD_WIKI_COLLECTION"

or, when a specific page path is known:

${QMD_CLI:-qmd} get "qmd://$QMD_WIKI_COLLECTION/<page>.md" -l 5

Record one of:

• QMD refreshed: update + embed + verified
• QMD refreshed: update only + verified
• QMD skipped: QMD_WIKI_COLLECTION unset
• QMD skipped: qmd CLI unavailable
• QMD failed: <short error summary>