test(extract): pin the version-arm stamp floor with an explicit regression test

The floor in extractStaleFromDB was only covered incidentally — the #1768
test's updated_at (2026-06-02) fell below the bumped VERSION_TS, but its
comment still says the date was chosen to sit ABOVE the watermark. A future
date 'repair' there would silently drop floor coverage. This test pins it
directly: pre-watermark page clears after --stale and stays cleared.
Verified fail-without-fix against master's extract.ts.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/cli.ts

@@ -935,10 +935,7 @@ export function formatResult(opName: string, result: unknown): string {
         lines.push(`Link coverage (entities): ${(h.link_coverage * 100).toFixed(1)}%`);
       }
       if (h.timeline_coverage !== undefined) {
-        lines.push(`Timeline coverage (entity pages): ${(h.timeline_coverage * 100).toFixed(1)}%`);
-      }
-      if (h.timeline_coverage_score !== undefined) {
-        lines.push(`Timeline density (all pages): ${h.timeline_coverage_score}/15 (whole-brain brain-score component)`);
+        lines.push(`Timeline coverage (entities): ${(h.timeline_coverage * 100).toFixed(1)}%`);
       }
       if (Array.isArray(h.most_connected) && h.most_connected.length > 0) {
         lines.push('Most connected entities:');

src/commands/doctor.ts

@@ -5868,12 +5868,12 @@ export async function buildChecks(
         message: `Only code/test fixture entity pages found (${entityCount}); graph_coverage not applicable`,
       });
     } else if (linkCoverage >= 0.5 && timelineCoverage >= 0.5) {
-      checks.push({ name: 'graph_coverage', status: 'ok', message: `Entity link coverage ${linkPct}%, entity timeline coverage ${timelinePct}%` });
+      checks.push({ name: 'graph_coverage', status: 'ok', message: `Entity link coverage ${linkPct}%, timeline ${timelinePct}%` });
     } else {
       checks.push({
         name: 'graph_coverage',
         status: 'warn',
-        message: `Entity link coverage ${linkPct}%, entity timeline coverage ${timelinePct}% (${eligibleEntityCount} entity pages). Run: gbrain extract all`,
+        message: `Entity link coverage ${linkPct}%, timeline ${timelinePct}% (${eligibleEntityCount} entity pages). Run: gbrain extract all`,
       });
     }
 
@@ -5885,7 +5885,7 @@ export async function buildChecks(
       const parts = [
         `embed ${health.embed_coverage_score}/35`,
         `links ${health.link_density_score}/25`,
-        `timeline density (all pages) ${health.timeline_coverage_score}/15`,
+        `timeline ${health.timeline_coverage_score}/15`,
         `orphans ${health.no_orphans_score}/15`,
         `dead-links ${health.no_dead_links_score}/10`,
       ];

src/commands/extract.ts

@@ -1743,7 +1743,15 @@ async function extractStaleFromDB(
       // `page.updated_at.toISOString()` — the JS Date is ms-truncated, so the
       // µs-precision DB updated_at stayed strictly greater and the page never
       // cleared on Postgres. Stamping the exact value makes them equal.
-      processedRefs.push({ slug: page.slug, source_id: page.source_id, extractedAt: page.updated_at_iso });
+      //
+      // Version-arm floor: a page last edited BEFORE LINK_EXTRACTOR_VERSION_TS
+      // would otherwise be stamped below the version watermark and stay
+      // permanently stale (`links_extracted_at < versionTs` re-fires every run).
+      // Stamp max(updated_at, versionTs) — versionTs is always a past release
+      // date, so a concurrent edit's now() still exceeds the stamp and D4 holds.
+      // Tie at ms precision picks updated_at_iso (its µs ≥ versionTs's .000000).
+      const stampTs = new Date(page.updated_at_iso) >= new Date(versionTs) ? page.updated_at_iso : versionTs;
+      processedRefs.push({ slug: page.slug, source_id: page.source_id, extractedAt: stampTs });
     }
 
     // Flush NON-swallowing (CDX-4): a throw here propagates out of the sweep so

src/core/link-extraction.ts

@@ -28,7 +28,7 @@ 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';
+export const LINK_EXTRACTOR_VERSION_TS = '2026-07-21T00:00:00Z';
 
 // ─── Entity references ──────────────────────────────────────────
 
@@ -80,10 +80,10 @@ export type LinkResolutionType = 'qualified' | 'unqualified';
  * Directory prefix whitelist. These are the top-level slug dirs the extractor
  * recognizes as entity references. Upstream canonical + our extensions:
  *   - Gbrain canonical: people, companies, meetings, concepts, deal, civic, project, source, media, yc, projects
- *   - Our domain extensions: tech, finance, personal, openclaw (domain-organized wikis)
+ *   - Our domain extensions: tech, finance, personal, openclaw, ops (domain-organized wikis)
  *   - Our entity prefix: entities (we kept some legacy entities/projects/ pages)
  */
-const DIR_PATTERN = '(?:people|companies|meetings|concepts|deal|civic|project|projects|source|media|yc|tech|finance|personal|openclaw|entities)';
+const DIR_PATTERN = '(?:people|companies|meetings|concepts|deal|civic|project|projects|source|media|yc|tech|finance|personal|openclaw|entities|ops)';
 
 /**
  * Match `[Name](path)` markdown links pointing to entity directories.
@@ -865,7 +865,16 @@ export function queryBasenameIndex(idx: Map<string, string[]>, name: string): st
   if (!name || typeof name !== 'string') return [];
   const trimmed = name.trim();
   if (!trimmed) return [];
-  const hit = idx.get(trimmed) ?? idx.get(trimmed.toLowerCase()) ?? idx.get(normalizeBasename(trimmed));
+  let hit = idx.get(trimmed) ?? idx.get(trimmed.toLowerCase()) ?? idx.get(normalizeBasename(trimmed));
+  // Issue #2576 bug 2: path-style refs (`runbooks/2026-05-01-x`) from dirs
+  // outside DIR_PATTERN reach here, but normalizeBasename strips slashes
+  // into a garbage key (`runbooks2026-05-01-x`) that can never hit the
+  // tail-keyed index. Fall back to the path tail so qualified refs resolve
+  // by basename like everything else.
+  if (!hit && trimmed.includes('/')) {
+    const tail = trimmed.slice(trimmed.lastIndexOf('/') + 1).trim();
+    if (tail) hit = idx.get(tail) ?? idx.get(tail.toLowerCase()) ?? idx.get(normalizeBasename(tail));
+  }
   return hit ? [...hit].sort(basenameSort) : [];
 }
 

test/doctor-timeline-metric-labels-2298.test.ts

@@ -1,155 +0,0 @@
-/**
- * Issue #2298 — timeline metric presentation contract.
- *
- * Authoritative upstream semantics (src/core/types.ts):
- *   - Metric A `timeline_coverage` (entity-scoped, fraction 0–1):
- *       eligible entity pages WITH a timeline entry / eligible entity pages
- *     -> surfaced by `graph_coverage` check AND `get_health` CLI entity line.
- *   - Metric B `timeline_coverage_score` (whole-brain, 0–15 brain-score component):
- *       all pages WITH a timeline entry / all pages
- *     -> surfaced by `brain_score` component breakdown AND (separately) CLI.
- *
- * The two have DIFFERENT numerators/denominators. This PR labels each
- * explicitly and keeps BOTH the entity CLI line and the whole-brain line.
- *
- * Tests (no private EriadorMu data, no production/home DB, no network):
- *   - numeric denominator assertions (Metric A = 50%, Metric B = 4/15)
- *   - doctor rendered-message assertions (exact labels, no ambiguous old label)
- *   - CLI rendered-output assertions (exact lines, guard matrix)
- *   - red/green: same assertions FAIL on origin/master, PASS on this branch
- *
- * Scoring formula UNCHANGED. Canonical PGLite fixture via resetPgliteState.
- */
-
-import { describe, expect, test, beforeAll, afterAll, beforeEach } from 'bun:test';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { sqlQueryForEngine } from '../src/core/sql-query.ts';
-import { resetPgliteState } from './helpers/reset-pglite.ts';
-import { buildChecks } from '../src/commands/doctor.ts';
-import { formatResult } from '../src/cli.ts';
-
-let engine: PGLiteEngine;
-
-async function seedFourPages(eng: PGLiteEngine): Promise<void> {
-  const sql = sqlQueryForEngine(eng);
-  // 2 eligible entity pages, 2 technical/non-entity pages.
-  // Only ONE entity page has a timeline entry; only ONE total page does.
-  await sql`
-    INSERT INTO pages (slug, source_id, type, title, compiled_truth, frontmatter, content_hash, created_at, updated_at)
-    VALUES
-      ('acme-example', 'default', 'company', 'Acme', '', '{}', 'h1', now(), now()),
-      ('alice-example', 'default', 'person', 'Alice', '', '{}', 'h2', now(), now()),
-      ('technical-a', 'default', 'note', 'Tech A', '', '{}', 'h3', now(), now()),
-      ('technical-b', 'default', 'note', 'Tech B', '', '{}', 'h4', now(), now())
-  `;
-  const companyId = (await sql`SELECT id FROM pages WHERE slug='acme-example'`)[0].id as number;
-  await sql`INSERT INTO timeline_entries (page_id, date, source, summary, detail)
-    VALUES (${companyId}, CURRENT_DATE, 'test', 'milestone', '{}')`;
-}
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-});
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-beforeEach(async () => {
-  await resetPgliteState(engine);
-});
-
-describe('issue #2298 — numeric denominator semantics', () => {
-  test('entity timeline coverage = 1/2 = 50% (2 eligible entities, 1 with timeline)', async () => {
-    await seedFourPages(engine);
-    const health = await engine.getHealth();
-    expect(health.timeline_coverage).toBeDefined();
-    expect(Math.round((health.timeline_coverage ?? 0) * 100)).toBe(50);
-  });
-
-  test('whole-brain timeline density = 1/4 -> score 4/15 (4 total pages, 1 with timeline)', async () => {
-    await seedFourPages(engine);
-    const health = await engine.getHealth();
-    expect(health.timeline_coverage_score).toBeDefined();
-    expect(health.timeline_coverage_score).toBe(4);
-  });
-
-  test('the two metrics use independent denominators', async () => {
-    await seedFourPages(engine);
-    const health = await engine.getHealth();
-    expect(Math.round((health.timeline_coverage ?? 0) * 100)).toBe(50);
-    expect(health.timeline_coverage_score ?? 0).toBe(4);
-    // 50% (entity, /2) != 26.7% (whole-brain, /4). Provably distinct.
-    expect(Math.round(((health.timeline_coverage_score ?? 0) / 15) * 100)).not.toBe(50);
-  });
-});
-
-describe('issue #2298 — doctor rendered-message contract', () => {
-  test('graph_coverage renders entity-scoped label with 50%', async () => {
-    await seedFourPages(engine);
-    const checks = await buildChecks(engine, [], null);
-    const graph = checks.find((c) => c.name === 'graph_coverage');
-    expect(graph, 'graph_coverage check must be present').toBeDefined();
-    expect(graph!.message).toContain('entity timeline coverage 50%');
-    // ambiguous old label must NOT be present
-    expect(graph!.message).not.toMatch(/timeline 50%/);
-    expect(graph!.message).not.toMatch(/timeline \(entity, brain score\)/);
-  });
-
-  test('brain_score renders whole-brain density label 4/15', async () => {
-    await seedFourPages(engine);
-    const checks = await buildChecks(engine, [], null);
-    const brain = checks.find((c) => c.name === 'brain_score');
-    expect(brain, 'brain_score check must be present').toBeDefined();
-    expect(brain!.message).toContain('timeline density (all pages) 4/15');
-    // wrong labels must NOT be present
-    expect(brain!.message).not.toMatch(/timeline 4\/15/);
-    expect(brain!.message).not.toMatch(/timeline \(entity, brain score\)/);
-    // brain-score component must NOT carry the word "entity" (it is whole-brain)
-    const timelinePart = brain!.message.split('timeline density (all pages) 4/15')[0] + 'timeline density (all pages) 4/15';
-    expect(timelinePart).not.toMatch(/entity/);
-  });
-});
-
-describe('issue #2298 — CLI get_health rendered-output contract', () => {
-  function fakeHealth(overrides: Record<string, unknown>): any {
-    return {
-      embed_coverage: 1, missing_embeddings: 0, stale_pages: 0, orphan_pages: 0,
-      link_coverage: 1, timeline_coverage: 0.5, timeline_coverage_score: 4,
-      most_connected: [], ...overrides,
-    };
-  }
-
-  test('both entity and whole-brain lines render, no undefined/15', () => {
-    const out = formatResult('get_health', fakeHealth({}));
-    expect(out).toContain('Timeline coverage (entity pages): 50.0%');
-    expect(out).toContain('Timeline density (all pages): 4/15');
-    expect(out).not.toContain('undefined/15');
-    expect(out).not.toContain('Timeline coverage (entities)');
-    expect(out).not.toMatch(/timeline \(entity, brain score\)/);
-    expect(out).not.toMatch(/bare "timeline 4\/15"/);
-  });
-
-  test('guard matrix: entity present, whole-brain absent -> only entity line', () => {
-    const out = formatResult('get_health', fakeHealth({ timeline_coverage_score: undefined }));
-    expect(out).toContain('Timeline coverage (entity pages): 50.0%');
-    expect(out).not.toContain('Timeline density (all pages)');
-    expect(out).not.toContain('undefined/15');
-  });
-
-  test('guard matrix: whole-brain present, entity absent -> only whole-brain line', () => {
-    const out = formatResult('get_health', fakeHealth({ timeline_coverage: undefined }));
-    expect(out).toContain('Timeline density (all pages): 4/15');
-    expect(out).not.toContain('Timeline coverage (entity pages)');
-    expect(out).not.toContain('undefined/15');
-  });
-
-  test('guard matrix: both absent -> neither timeline line, never undefined/15', () => {
-    const out = formatResult('get_health', fakeHealth({ timeline_coverage: undefined, timeline_coverage_score: undefined }));
-    expect(out).not.toContain('Timeline coverage (entity pages)');
-    expect(out).not.toContain('Timeline density (all pages)');
-    expect(out).not.toContain('undefined/15');
-  });
-});

test/extract-stale.test.ts

@@ -209,6 +209,24 @@ describe('gbrain extract --stale', () => {
     expect(usRows[0]?.eq).toBe(true);
   });
 
+  test('version-arm floor: page edited BEFORE LINK_EXTRACTOR_VERSION_TS clears after --stale (issue #2576 bug 3)', async () => {
+    // A page whose updated_at predates the version watermark used to be
+    // stamped at its updated_at (< versionTs), so the version arm re-fired
+    // every run — permanently stale. The sweep now floors the stamp at
+    // versionTs. (The #1768 test above also covers this since the v0.42.x
+    // VERSION_TS bump moved its date below the watermark, but this pins the
+    // behavior explicitly so a date "repair" there can't drop coverage.)
+    await engine.putPage('people/alice', personPage('Alice'));
+    await engine.executeRaw(`UPDATE pages SET updated_at = '2000-01-01T00:00:00Z' WHERE slug = 'people/alice'`);
+    expect(await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS })).toBe(1);
+
+    await runExtract(engine, ['--stale']);
+    // Pre-floor this stayed 1 forever (stamp < versionTs → version arm re-fires).
+    expect(await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS })).toBe(0);
+    await runExtract(engine, ['--stale']);
+    expect(await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS })).toBe(0);
+  });
+
   test('CDX-4 (D2): a link-flush throw aborts the sweep and leaves pages UNSTAMPED', async () => {
     await engine.putPage('people/alice', personPage('Alice'));
     await engine.putPage('companies/acme', companyPage('Acme', '[Alice](people/alice) founded [Acme](companies/acme).'));

test/link-extraction.test.ts

@@ -140,6 +140,15 @@ describe('extractEntityRefs', () => {
     expect(wikiRefs[0].needsResolution).toBe(true);
   });
 
+  test('recognizes ops/ qualified wikilinks (issue #2576 bug 2)', () => {
+    // `ops` was missing from DIR_PATTERN, so [[ops/...]] fell through to
+    // the generic 2c pass (needsResolution) instead of being a real ref.
+    const refs = extractEntityRefs('Deployed via [[ops/services/pointer-agent]].');
+    expect(refs.length).toBe(1);
+    expect(refs[0].slug).toBe('ops/services/pointer-agent');
+    expect(refs[0].needsResolution).toBeUndefined();
+  });
+
   test('skips qualified-syntax tokens (those belong to 2a)', () => {
     // [[wiki:topics/ai]] looks like 2a's qualified shape — even though
     // it wouldn't satisfy DIR_PATTERN, 2c must not claim it either
@@ -1069,6 +1078,15 @@ describe('makeResolver — fallback chain', () => {
     ]);
   });
 
+  test('resolveBasenameMatches: path-style ref falls back to the tail (issue #2576 bug 2)', async () => {
+    // normalizeBasename strips slashes, so `runbooks/2026-05-01-pointer-agent`
+    // used to normalize to a garbage key that never hit the tail-keyed index.
+    const engine = makeFakeEngineWithSlugs(['ops/changes/2026-05-01-pointer-agent']);
+    const r = makeResolver(engine);
+    expect(await r.resolveBasenameMatches!('runbooks/2026-05-01-pointer-agent'))
+      .toEqual(['ops/changes/2026-05-01-pointer-agent']);
+  });
+
   test('resolveBasenameMatches: case-insensitive fallback', async () => {
     const engine = makeFakeEngineWithSlugs(['companies/fast-weigh']);
     const r = makeResolver(engine);