The garrytan#972 feature shipped with no user-facing docs — only CHANGELOG + CLAUDE.md.
Anyone migrating an Obsidian/Notion vault with bare [[name]] wikilinks couldn't
discover the link_resolution.global_basename flag unless gbrain doctor happened
to surface its hint.

- README "Self-wiring knowledge graph": one sentence on the opt-in mode for
  Obsidian-style cross-folder bare wikilinks + the doctor pre-check, linking to
  the install step.
- INSTALL_FOR_AGENTS Step 4.5 (Wire the Knowledge Graph): a dedicated agent-
  facing subsection — when bare [[name]] links need it, the enable command,
  re-running extract, the doctor opportunity hint, and the multi-match behavior.
- Regenerated llms-full.txt.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…ame-wikilinks

The fork's master (ukd1, v0.41.31.0) trailed upstream by two releases
(v0.41.32.0 staleness fix + v0.41.33.0 adaptive return-sizing), both of which
collided with this branch. Synced to real upstream so PR garrytan#1388 merges clean.

Re-resolutions on top of the prior merge:
- Version: upstream used 0.41.32.0; bumped to 0.41.34.0 (next after 0.41.33.0).
- Migration: upstream claimed v109 (sources_newest_content_at); our
  links_link_source_widen renumbered v109 → v110. Full-union CHECK
  ('markdown','frontmatter','manual','mentions','wikilink-resolved') preserved.
- CHANGELOG: our 0.41.34.0 entry on top, upstream's 0.41.33.0 + 0.41.32.0 below.
- schema-embedded.ts + llms-full.txt regenerated; link_source union verified
  intact in schema.sql + pglite-schema.ts after auto-merge.

Verified: typecheck clean, privacy/jsonb/source-id guards pass, 369 surface
tests (migrate/link-extraction/extract-fs/doctor) + 7 global-basename E2E green;
migrations apply [109] sources_newest_content_at → [110] wikilink-basename.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…lay text

Codex outside-voice [P1]: `[[struktura|the project]]` resolved the basename
"the project" (the alias) instead of `struktura` (the target), because
extractPageLinks called resolveBasenameMatches(ref.name) and the doctor check
keyed basenameIndex.get(e.name). ref.name is the display alias (match[2]);
ref.slug is the wikilink target (match[1]).

- extractPageLinks resolves ref.slug; context excerpt locates ref.slug.
- doctor link_resolution_opportunity keys e.slug so its estimate matches
  what extraction actually resolves.
- Test: aliased wikilink calls resolveBasenameMatches with the target, never
  the display text.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…-link

Codex outside-voice [P1]: put_page's reconcilableOut filter excluded
link_source='wikilink-resolved', so a basename edge written by auto-link
survived after the bare wikilink was deleted from the page OR the
link_resolution.global_basename flag was turned off (the stale-removal loop
only iterates reconcilableOut). Add 'wikilink-resolved' to the reconcilable
set; manual edges still untouched.

Test: write page with [[struktura]] (flag on) → edge lands; re-put without
the wikilink → edge reconciled away.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…edges)

Codex outside-voice [P1]: makeResolver.resolveBasenameMatches called
engine.getAllSlugs() unscoped, so a bare [[name]] could resolve to a
same-tail page in a DIFFERENT source and create a cross-source edge. The
engine exposes getAllSlugs({sourceId}) precisely to prevent this. garrytan#972 is
"global basename across folders," not "cross-source federation" — the
canonical gbrain multi-source bug class.

- makeResolver gains opts.sourceId; ensureBasenameIndex passes it to
  getAllSlugs (unscoped only when sourceId omitted — back-compat).
- runAutoLink (put_page) passes opts.sourceId; extractLinksFromDB passes
  sourceIdFilter. FS extract is already single-source (walks one dir).
- Tests: scoped index returns only the source's slugs (no cross-source);
  unscoped call stays brain-wide.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…nk-resolved'

The FS extract path is the issue's default repro (gbrain extract links with no
--source db). ExtractedLink had no link_source field, so FS basename edges
landed with the engine default ('markdown') instead of the 'wikilink-resolved'
provenance the DB / put_page paths set and the docs promise. The e2e FS test
only asserted link_type, so it was blind to this.

- ExtractedLink gains link_source?; extractLinksFromFile sets it to
  'wikilink-resolved' on basename edges (undefined for ordinary markdown).
- Carries through the addLinksBatch snapshots automatically (LinkBatchInput
  already has link_source); single-row addLink fallback now passes it too.
- e2e FS repro asserts link_source === 'wikilink-resolved'.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…S/doctor

Codex outside-voice [P2] DRY: three surfaces each hand-rolled a basename
matcher with divergent key sets — the doctor omitted the slugified key, so its
link_resolution_opportunity estimate undercounted what extraction resolves, and
the resolver returned matches in unsorted getAllSlugs bucket order.

New shared exports in link-extraction.ts: buildBasenameIndex(slugs) +
queryBasenameIndex(index, name) (keys raw/lower/slugified tail; stable sort
shorter-first then lexical) + normalizeBasename.

- makeResolver.resolveBasenameMatches → queryBasenameIndex (now stable-sorted).
- extract.ts resolveBasenameMatchesFromSlugs → delegates to the shared pair.
- doctor link_resolution_opportunity → shared builder/query (slugified key
  added; estimate now matches extraction).
- Test: doctor counts a slugified-only match ([[Fast Weigh]] → companies/fast-weigh).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

… decision

Codex outside-voice P2 findings:
- P2a markdown-label masking: a wikilink inside a markdown-link label
  ([see [[acme]]](companies/acme.md)) spawned a stray generic basename ref.
  Pass-1 can't match the nested brackets, so a new MARKDOWN_LABEL_WIKILINK_RE
  masks those spans out of pass 2c. Inner [[acme]] is now inert.
- P2b FS code-fence: the FS path (extractMarkdownLinks on raw content) didn't
  strip code blocks like the DB path. extractLinksFromFile now scans
  stripCodeBlocks(content) so [[name]] inside a fence creates no FS edge.
- P2c self-link guard: a basename [[own-tail]] on its own page resolved back
  to itself. Dropped in both extractPageLinks and the FS path.
- P2d dedup: documented the decision to KEEP qualified + bare edges to the
  same target as separate rows (distinct provenance/audit trail).
- P2e: skipFrontmatter unresolved-contract tests added.

Tests: P2a inert-label, P2c self-link drop, P2b code-fence, P2e unresolved.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

The check did listAllPageRefs() + a getPage() per page under a 60s budget.
On a large brain (the eng-review concern) it hit the budget every non-fast
doctor run and returned a perpetual partial, adding ~60s.

Now batch-loads the 1000 most-recent pages in ONE query
(ORDER BY id DESC LIMIT SAMPLE_LIMIT) and scans in memory, with the 60s cap
kept as a backstop. Mirrors the v0.40.9 sampling convention. The estimate
message names the bound when the brain exceeds the sample
("scanned the 1000 most-recent of N pages").

Test: source-grep pins the bounded query + the absence of the per-page
getPage walk.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…112 / 0.42.6.0

Merge churn left intermediate refs: schema.sql + schema-embedded.ts said
"migration v93", CLAUDE.md said "v0.41.32.0 / Migration v109", CHANGELOG said
"Migration v93". Reconciled all to migration v112 / shipping 0.42.6.0. The
CLAUDE.md annotation is also refreshed to describe the final behavior (shared
matcher, source-scoping, alias-by-target, stale-edge reconciliation, bounded
doctor scan) and credit @rayers + @ukd1. Regenerated schema-embedded + llms.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Second re-sync onto current master to ship garrytan#972 as v0.42.10.0.

- VERSION/package.json -> 0.42.10.0 (buffer over master's 0.42.8.0 for queue
  collisions, per request).
- CHANGELOG: our 0.42.10.0 entry on top; master's 0.42.8.0/0.42.7.0/0.42.6.0
  history preserved below.
- Migration collision: master claimed v112 (pages_links_extracted_at, garrytan#1696),
  so our links_link_source_widen renumbered v112 -> v113. Full-union CHECK
  preserved (markdown/frontmatter/manual/mentions/wikilink-resolved).
- extract.ts: unioned imports (master's LINK_EXTRACTOR_VERSION_TS/LinkCandidate
  + our buildBasenameIndex/queryBasenameIndex/stripCodeBlocks).
- doctor.test.ts: kept both garrytan#972 link_resolution describe and master's garrytan#1699
  quarantine/flagged describe.
- CLAUDE.md: de-glommed import-file line, kept master's garrytan#1699 entries + our
  garrytan#972 annotation (v0.42.10.0 / migration v113).
- schema.sql comment v112 -> v113; schema-embedded + llms regenerated.
- typecheck clean.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>