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/commands/autopilot-fanout.ts

@@ -186,18 +186,6 @@ export function isSourceStale(src: SourceRow, now = Date.now(), floorMin = FULL_
   return ageMin >= floorMin;
 }
 
-/**
- * #2060: count sources past the per-source cycle freshness floor. Consumed
- * by autopilot's dispatch decision — a stale source forces the fanout path
- * even when the doctor plan is small (score 70–94, plan ≤ 3, est < 300s),
- * so targeted mode can't leave cycle_freshness stale indefinitely.
- * dispatchPerSource's own throttles (skipped_fresh / fanoutMax / failure
- * cooldown) bound the resulting work.
- */
-export function countStaleSources(sources: SourceRow[], now = Date.now(), floorMin = FULL_CYCLE_FLOOR_MIN): number {
-  return sources.filter((s) => isSourceStale(s, now, floorMin)).length;
-}
-
 /**
  * Most recent SUCCESSFUL cycle for a source. Prefers `last_source_cycle_at`
  * (per-source phases, written by the split cycle) and falls back to the legacy

src/commands/autopilot.ts

@@ -901,27 +901,13 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         const FULL_CYCLE_FLOOR_MIN = 60;
         const minutesSinceLastFull = (Date.now() - lastFullCycleAt) / 60000;
 
-        // #2060: stale per-source cycle freshness is a dispatch input. Without
-        // it, a brain sitting at score 70–94 with a small targeted plan (≤3
-        // steps, <300s) stays in targeted mode indefinitely and no per-source
-        // cycle is ever dispatched — cycle_freshness never advances. A stale
-        // source forces the fanout path; dispatchPerSource's throttles
-        // (skipped_fresh / fanoutMax / failure cooldown) bound the work.
-        // Fail-open to 0: a read failure must not block dispatch.
-        let staleCycleSources = 0;
-        try {
-          const { countStaleSources } = await import('./autopilot-fanout.ts');
-          staleCycleSources = countStaleSources(await engine.listAllSources({ localPathOnly: true }));
-        } catch { /* fail-open: freshness is a dispatch hint, not a gate */ }
-
         const shouldFullCycle =
           (score >= 95 && plan.length === 0 && minutesSinceLastFull >= FULL_CYCLE_FLOOR_MIN) ||
           plan.length > 3 ||
           estTotal >= 300 ||
-          score < 70 ||
-          staleCycleSources > 0;
+          score < 70;
 
-        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN && staleCycleSources === 0;
+        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN;
 
         if (shouldSleep) {
           if (jsonMode) {

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/cycle.ts

@@ -854,10 +854,7 @@ interface SyncPhaseResult extends PhaseResult {
 /**
  * Resolve the source id for a brain directory by looking up the sources
  * table. Returns undefined when no registered source matches (falls back
- * to pre-v0.18 global config.sync.* keys) OR when MORE than one source
- * claims the path — an ambiguous match must not scope phases or stamp
- * last_full_cycle_at for an arbitrarily-picked source (the "freshness
- * stamp that lies" this resolution exists to prevent).
+ * to pre-v0.18 global config.sync.* keys).
  */
 async function resolveSourceForDir(
   engine: BrainEngine,
@@ -868,10 +865,10 @@ async function resolveSourceForDir(
   if (brainDir === null) return undefined;
   try {
     const rows = await engine.executeRaw<{ id: string }>(
-      `SELECT id FROM sources WHERE local_path = $1 LIMIT 2`,
+      `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`,
       [brainDir],
     );
-    return rows.length === 1 ? rows[0]!.id : undefined;
+    return rows[0]?.id;
   } catch {
     // sources table might not exist on very old brains — fall through.
     return undefined;
@@ -2368,23 +2365,17 @@ export async function runCycle(
   }
 
   // v0.38 (codex r1 P0-5): persist per-source cycle completion timestamp
-  // when the cycle ran successfully against a resolvable source. Read by
-  // autopilot's per-source freshness gate next tick.
-  //
-  // #1993: keyed off `cycleSourceId` (opts.sourceId ?? the source resolved
-  // from brainDir) — the SAME id the cycle locked + scoped its phases to —
-  // NOT raw opts.sourceId. The autopilot's inline cycle sets brainDir but
-  // passes no explicit sourceId, so keying off opts.sourceId alone never
-  // advanced last_full_cycle_at and cycle_freshness stayed stale even while
-  // the autopilot cycled every interval. Skipped when:
-  //   - no source resolves (engine null, or no checkout AND no opts.sourceId)
+  // when the cycle ran successfully against an explicit source. Read by
+  // autopilot's per-source freshness gate next tick. Skipped when:
+  //   - opts.sourceId is unset (legacy callers — autopilot still here)
+  //   - engine is null (no-DB path)
   //   - status is 'failed' or 'skipped' (don't mark a non-run as fresh)
   //   - dryRun (writes are out of scope)
   //
   // Best-effort: a write failure does NOT change the CycleReport status.
   // The cost of writing the wrong timestamp post-failure is higher than
   // the cost of missing a successful write (next cycle will redo work).
-  if (cycleSourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
+  if (opts.sourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
     try {
       const nowIso = new Date().toISOString();
       // #2194 fix #3 (the cycle split): `last_source_cycle_at` is the NEW gate
@@ -2394,13 +2385,13 @@ export async function runCycle(
       // phases (those gate on autopilot.last_global_at), so writing it on a
       // source-only cycle does not re-introduce the freshness poisoning codex
       // flagged in the rejected skip-based design.
-      await engine.updateSourceConfig(cycleSourceId, {
+      await engine.updateSourceConfig(opts.sourceId, {
         last_source_cycle_at: nowIso,
         last_full_cycle_at: nowIso,
       });
     } catch (e) {
       // Best-effort; cycle already succeeded by the time we get here.
-      console.warn(`[cycle] failed to write last_source_cycle_at for source ${cycleSourceId}: ${e instanceof Error ? e.message : String(e)}`);
+      console.warn(`[cycle] failed to write last_source_cycle_at for source ${opts.sourceId}: ${e instanceof Error ? e.message : String(e)}`);
     }
   }
 

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/autopilot-fanout-wiring.test.ts

@@ -54,20 +54,6 @@ describe('autopilot.ts ↔ dispatchPerSource wiring', () => {
     expect(AUTOPILOT_SRC).toMatch(/lastFullCycleAt\s*=\s*Date\.now\(\)/);
   });
 
-  test('stale per-source cycle freshness is a shouldFullCycle input (#2060)', () => {
-    // Targeted mode (score 70–94, plan ≤3, est <300s) must not be able to
-    // starve per-source cycle dispatch: a stale source (per countStaleSources
-    // over listAllSources) forces the fanout path, and the sleep gate must
-    // not fire while stale sources exist. Without these terms, cycle
-    // freshness never advances for a brain that always lands in targeted mode.
-    expect(AUTOPILOT_SRC).toMatch(/countStaleSources/);
-    const fullCycleDeclIdx = AUTOPILOT_SRC.indexOf('const shouldFullCycle');
-    expect(fullCycleDeclIdx).toBeGreaterThan(-1);
-    const decl = AUTOPILOT_SRC.slice(fullCycleDeclIdx, fullCycleDeclIdx + 700);
-    expect(decl).toMatch(/staleCycleSources\s*>\s*0/);
-    expect(decl).toMatch(/const shouldSleep[^;]*staleCycleSources\s*===\s*0/);
-  });
-
   test('does NOT regress to the single-job dispatch on the full-cycle path', () => {
     // Pre-PR: the shouldFullCycle branch did:
     //   const job = await queue.add('autopilot-cycle', { repoPath }, {

test/autopilot-fanout.test.ts

@@ -14,7 +14,6 @@ import { describe, test, expect } from 'bun:test';
 import {
   readLastFullCycleAt,
   isSourceStale,
-  countStaleSources,
   selectSourcesForDispatch,
   resolveFanoutMax,
   dispatchPerSource,
@@ -75,23 +74,6 @@ describe('isSourceStale', () => {
   });
 });
 
-describe('countStaleSources (#2060 dispatch-decision input)', () => {
-  const NOW = Date.parse('2026-05-22T12:00:00.000Z');
-  test('counts never-cycled + past-floor sources, ignores fresh', () => {
-    const sources = [
-      src('never-cycled'), // stale (null)
-      src('old', new Date(NOW - 2 * 60 * 60_000).toISOString()), // stale (2h)
-      src('fresh', new Date(NOW - 30 * 60_000).toISOString()), // fresh (30min)
-    ];
-    expect(countStaleSources(sources, NOW)).toBe(2);
-  });
-  test('returns 0 for all-fresh and for empty list', () => {
-    const fresh = src('a', new Date(NOW - 10 * 60_000).toISOString());
-    expect(countStaleSources([fresh], NOW)).toBe(0);
-    expect(countStaleSources([], NOW)).toBe(0);
-  });
-});
-
 describe('selectSourcesForDispatch', () => {
   const NOW = Date.parse('2026-05-22T12:00:00.000Z');
   const fresh = (id: string, agoMin: number) =>

test/cycle-last-full-cycle-at.test.ts

@@ -3,10 +3,8 @@
  * cycles. Closes codex round-1 P0-5 (write site for last_full_cycle_at
  * was unspecified pre-PR).
  *
- * Conditions for write (keyed off `cycleSourceId` = opts.sourceId ?? the
- * source resolved from brainDir, so the autopilot's inline cycle — brainDir
- * set, no explicit sourceId — also advances the timestamp, #1993):
- *   - a source resolves (explicit sourceId, or brainDir matches a source)
+ * Conditions for write:
+ *   - opts.sourceId is set (legacy callers without sourceId skip the write)
  *   - engine is non-null (no-DB path skips)
  *   - status is 'ok' | 'clean' | 'partial' (failed/skipped don't mark fresh)
  *   - dryRun is false
@@ -92,45 +90,17 @@ describe('runCycle last_full_cycle_at exit hook', () => {
     });
   });
 
-  test('no explicit sourceId but brainDir resolves a source → writes the resolved source timestamp', async () => {
+  test('legacy caller (no sourceId) does NOT write any source timestamp', async () => {
     await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      // The autopilot's inline cycle sets brainDir but passes no sourceId.
-      // runCycle resolves the source from brainDir (local_path match) into
-      // cycleSourceId and stamps last_full_cycle_at for it — otherwise
-      // cycle_freshness reports the brain stale even while the autopilot
-      // cycles every interval (#1993).
-      await seedSource('resolved-from-dir'); // local_path = brainDir
-      expect(await readLastFullCycleAt('resolved-from-dir')).toBeNull();
-
-      const t0 = Date.now();
-      const report = await runCycle(engine, {
-        brainDir,
-        phases: ['lint'],
-      });
-      expect(['ok', 'clean']).toContain(report.status);
-
-      const after = await readLastFullCycleAt('resolved-from-dir');
-      expect(after).not.toBeNull();
-      expect(new Date(after!).getTime()).toBeGreaterThanOrEqual(t0);
-    });
-  });
-
-  test('no sourceId and brainDir matches no source → does not write', async () => {
-    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      // A source exists but its local_path does NOT match brainDir, so
-      // resolveSourceForDir returns undefined, cycleSourceId is undefined,
-      // and no per-source timestamp is written.
-      await engine.executeRaw(
-        `INSERT INTO sources (id, name, local_path, config, archived, created_at)
-         VALUES ('unmatched', 'unmatched', '/no/such/repo', '{}'::jsonb, false, NOW())
-         ON CONFLICT (id) DO UPDATE SET local_path = EXCLUDED.local_path`,
-        [],
-      );
+      await seedSource('default-like');
+      // No sourceId passed; should remain untouched.
       await runCycle(engine, {
         brainDir,
         phases: ['lint'],
       });
-      expect(await readLastFullCycleAt('unmatched')).toBeNull();
+      // No per-source write happens; default source's config stays empty.
+      const after = await readLastFullCycleAt('default-like');
+      expect(after).toBeNull();
     });
   });
 

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);