fix(extract): --stale sweep runs the real resolver — basename resolution reaches stale pages (#2576) (#2717)

extractStaleFromDB still used the pre-#972 `includeFrontmatter ? resolver :
nullResolver` ternary. The synthetic resolver has no resolveBasenameMatches,
so the gate in extractPageLinks skipped the issue-#972 bare-wikilink pass
regardless of link_resolution.global_basename — the sweep stamped every page
as extracted while silently dropping its [[bare-name]] links. Same brain,
same pages: `extract --stale` created 0 links where `extract links --source
db` created 218.

- Always pass the real batch resolver; gate passes via extractPageLinks opts
  ({ skipFrontmatter: !includeFrontmatter, globalBasename }), mirroring
  extractLinksFromDB — including the codex-[P1] sourceId scoping.
- Bump LINK_EXTRACTOR_VERSION_TS (documented protocol) so pages stamped by
  the broken sweep re-flag stale and re-extract under the fixed logic.
- Regression tests: bare wikilink resolves on --stale with the flag ON;
  still drops with the flag OFF (back-compat). The #1768 fixture now derives
  its updated_at from LINK_EXTRACTOR_VERSION_TS instead of a hardcoded date,
  so future version bumps can't silently flip its version arm.

Fixes bug 1 + bug 3 of #2576. Bug 2 (DIR_PATTERN gaps) is a separate
whitelist design call, intentionally not addressed here.

Co-authored-by: YMYD <53603073+OJ-OnJourney@users.noreply.github.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/commands/extract.ts

@@ -1684,9 +1684,17 @@ export async function extractStaleFromDB(
   // Batch mode = pg_trgm + exact only, NO per-name search fallback. The
   // resolution map sees ALL sources so qualified cross-source wikilinks resolve
   // even when --source-id scopes the stale SCAN.
-  const resolver = makeResolver(engine, { mode: 'batch' });
-  const nullResolver = { resolve: async () => null as string | null };
-  const activeResolver = includeFrontmatter ? resolver : nullResolver;
+  //
+  // #2576 bug 1: ALWAYS the real resolver — extractPageLinks's opts gate which
+  // pass runs (`skipFrontmatter` for the frontmatter pass, `globalBasename` for
+  // the issue-#972 bare-wikilink pass). The former `includeFrontmatter ?
+  // resolver : nullResolver` ternary predates #972; the synthetic resolver has
+  // no `resolveBasenameMatches`, so the --stale sweep silently skipped basename
+  // resolution even with `link_resolution.global_basename` enabled, stamping
+  // pages as extracted with their bare wikilinks dropped. Mirrors
+  // extractLinksFromDB (including the codex-[P1] `sourceId` scoping).
+  const resolver = makeResolver(engine, { mode: 'batch', sourceId: sourceIdFilter });
+  const globalBasename = await isGlobalBasenameEnabled(engine);
   const allRefs = await engine.listAllPageRefs();
   const allSlugs = new Set<string>();
   const slugToSources = new Map<string, string[]>();
@@ -1718,7 +1726,8 @@ export async function extractStaleFromDB(
     for (const page of rows) {
       const fullContent = page.compiled_truth + '\n' + page.timeline;
       const extracted = await extractPageLinks(
-        page.slug, fullContent, page.frontmatter, page.type, activeResolver,
+        page.slug, fullContent, page.frontmatter, page.type, resolver,
+        { skipFrontmatter: !includeFrontmatter, globalBasename },
       );
       for (const c of extracted.candidates) {
         const r = resolveCandidateSources(c, page.slug, page.source_id, allSlugs, slugToSources);

src/core/link-extraction.ts

@@ -28,7 +28,10 @@ import { ensureWellFormed } from './text-safe.ts';
  * OR updated_at > links_extracted_at`. It is an ISO-8601 string (NOT a number) —
  * the column is TIMESTAMPTZ and the predicate binds it as `::timestamptz`.
  */
-export const LINK_EXTRACTOR_VERSION_TS = '2026-05-31T00:00:00Z';
+// 2026-07-10: bumped for the #2576 --stale nullResolver fix — sweeps before it
+// stamped pages with their bare wikilinks silently dropped; the bump re-flags
+// them so the fixed sweep re-extracts.
+export const LINK_EXTRACTOR_VERSION_TS = '2026-07-10T00:00:00Z';
 
 // ─── Entity references ──────────────────────────────────────────
 

test/extract-stale.test.ts

@@ -186,9 +186,12 @@ describe('gbrain extract --stale', () => {
     // the precision gap is deterministic regardless of the engine's now() granularity.
     await engine.putPage('people/alice', personPage('Alice'));
     await engine.putPage('companies/acme', companyPage('Acme', '[Alice](people/alice) advises [Acme](companies/acme).'));
-    // Microsecond-precision updated_at, recent (after LINK_EXTRACTOR_VERSION_TS) so the
-    // version arm doesn't fire — the edited arm is what must clear.
-    await engine.executeRaw(`UPDATE pages SET updated_at = '2026-06-02 08:18:58.999166+00'`);
+    // Microsecond-precision updated_at, derived from LINK_EXTRACTOR_VERSION_TS
+    // (+2 days) so the version arm never fires regardless of future bumps —
+    // the edited arm is what must clear.
+    const afterVersionIso = new Date(Date.parse(LINK_EXTRACTOR_VERSION_TS) + 48 * 3600 * 1000).toISOString();
+    const usUpdatedAt = `${afterVersionIso.slice(0, 10)} ${afterVersionIso.slice(11, 19)}.999166+00`;
+    await engine.executeRaw(`UPDATE pages SET updated_at = '${usUpdatedAt}'`);
     expect(await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS })).toBe(2);
 
     await runExtract(engine, ['--stale']);
@@ -315,4 +318,48 @@ describe('gbrain extract --stale', () => {
     expect(exited).toBe(true);
     expect(msg).toContain('DB-source only');
   });
+
+  // ─── #2576 bug 1: --stale must run the same resolver passes as
+  // `extract links --source db` ─────────────────────────────────────────────
+
+  test('#2576: bare wikilink resolves via global_basename on the --stale path', async () => {
+    await engine.putPage('projects/struktura',
+      { type: 'project' as any, title: 'Struktura', compiled_truth: 'A project page.', timeline: '' });
+    await engine.putPage('concepts/knowledge-graph',
+      { type: 'concept' as any, title: 'Knowledge Graph',
+        compiled_truth: 'This concept relates to [[struktura]].', timeline: '' });
+    await engine.setConfig('link_resolution.global_basename', 'true');
+    try {
+      await runExtract(engine, ['--stale']);
+    } finally {
+      await engine.setConfig('link_resolution.global_basename', 'false');
+    }
+
+    // Pre-fix: the nullResolver (no resolveBasenameMatches) made
+    // extractPageLinks skip the basename pass, so the sweep stamped the page
+    // with the wikilink silently dropped — 0 links, watermark green.
+    const links = await engine.getLinks('concepts/knowledge-graph');
+    const strk = links.find(l => l.to_slug === 'projects/struktura');
+    expect(strk).toBeDefined();
+    expect(strk!.link_type).toBe('wikilink_basename');
+    // Still stamped like every processed page.
+    expect(await stampOf('concepts/knowledge-graph')).not.toBeNull();
+  });
+
+  test('#2576: bare wikilink still drops on --stale when global_basename is OFF (back-compat)', async () => {
+    await engine.putPage('projects/struktura',
+      { type: 'project' as any, title: 'Struktura', compiled_truth: 'A project page.', timeline: '' });
+    await engine.putPage('concepts/knowledge-graph',
+      { type: 'concept' as any, title: 'Knowledge Graph',
+        compiled_truth: 'This concept relates to [[struktura]].', timeline: '' });
+    await engine.setConfig('link_resolution.global_basename', 'false');
+
+    await runExtract(engine, ['--stale']);
+
+    expect((await engine.getLinks('concepts/knowledge-graph'))).toHaveLength(0);
+    // The gate lives in extractPageLinks opts now, not in a resolver swap —
+    // the page is still stamped either way.
+    expect(await stampOf('concepts/knowledge-graph')).not.toBeNull();
+  });
+
 });