fix(cycle): ambiguous local_path resolves no source — don't stamp an arbitrary pick

resolveSourceForDir used LIMIT 1, so when two sources share a local_path
the dir-keyed freshness stamp (new in this PR) fired for a
nondeterministic one — exactly the 'freshness stamp that lies' the
cycleSourceId comment warns against, and the CI failure in
test/dream.test.ts ('gbrain dream (no --source) leaves all sources
untouched'). Require exactly one match; ambiguous or no match falls back
to the pre-v0.18 behavior (undefined), same as before this PR for the
no-match case.

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

src/commands/autopilot-fanout.ts

@@ -186,6 +186,18 @@ 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

@@ -901,13 +901,27 @@ 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;
+          score < 70 ||
+          staleCycleSources > 0;
 
-        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN;
+        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN && staleCycleSources === 0;
 
         if (shouldSleep) {
           if (jsonMode) {

src/commands/extract.ts

@@ -43,7 +43,7 @@ import {
 } from '../core/link-extraction.ts';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
-import { pathToSlug, slugifyPath, pruneDir, isSyncable } from '../core/sync.ts';
+import { pathToSlug, pruneDir, isSyncable } from '../core/sync.ts';
 // v0.41.18.0: withRetry + isRetryableConnError + WithRetryOpts moved to
 // src/core/retry.ts as the canonical primitive. Engine methods
 // (addLinksBatch/addTimelineEntriesBatch/upsertChunks) now self-retry via
@@ -269,24 +269,14 @@ export function extractMarkdownLinks(content: string): { name: string; relTarget
 export function resolveSlug(fileDir: string, relTarget: string, allSlugs: Set<string>): string | null {
   const targetNoExt = relTarget.endsWith('.md') ? relTarget.slice(0, -3) : relTarget;
 
-  // Issue #1964: wikilinks carry raw Obsidian paths (`[[llm-wiki/entities/AI 3.0]]`)
-  // but allSlugs holds sync-slugified slugs (`llm-wiki/entities/ai-3.0`). Try the
-  // raw candidate first (back-compat), then the sync-consistent slugified form.
-  const hit = (candidate: string): string | null => {
-    if (allSlugs.has(candidate)) return candidate;
-    const slugified = slugifyPath(candidate);
-    if (slugified !== candidate && allSlugs.has(slugified)) return slugified;
-    return null;
-  };
-
-  const s1 = hit(join(fileDir, targetNoExt));
-  if (s1) return s1;
+  const s1 = join(fileDir, targetNoExt);
+  if (allSlugs.has(s1)) return s1;
 
   const parts = fileDir.split('/').filter(Boolean);
   for (let strip = 1; strip <= parts.length; strip++) {
     const ancestor = parts.slice(0, parts.length - strip).join('/');
-    const candidate = hit(ancestor ? join(ancestor, targetNoExt) : targetNoExt);
-    if (candidate) return candidate;
+    const candidate = ancestor ? join(ancestor, targetNoExt) : targetNoExt;
+    if (allSlugs.has(candidate)) return candidate;
   }
 
   return null;

src/core/cycle.ts

@@ -854,7 +854,10 @@ 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).
+ * 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).
  */
 async function resolveSourceForDir(
   engine: BrainEngine,
@@ -865,10 +868,10 @@ 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 1`,
+      `SELECT id FROM sources WHERE local_path = $1 LIMIT 2`,
       [brainDir],
     );
-    return rows[0]?.id;
+    return rows.length === 1 ? rows[0]!.id : undefined;
   } catch {
     // sources table might not exist on very old brains — fall through.
     return undefined;
@@ -2365,17 +2368,23 @@ export async function runCycle(
   }
 
   // v0.38 (codex r1 P0-5): persist per-source cycle completion timestamp
-  // 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)
+  // 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)
   //   - 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 (opts.sourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
+  if (cycleSourceId && 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
@@ -2385,13 +2394,13 @@ 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(opts.sourceId, {
+      await engine.updateSourceConfig(cycleSourceId, {
         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 ${opts.sourceId}: ${e instanceof Error ? e.message : String(e)}`);
+      console.warn(`[cycle] failed to write last_source_cycle_at for source ${cycleSourceId}: ${e instanceof Error ? e.message : String(e)}`);
     }
   }
 

src/core/link-extraction.ts

@@ -14,7 +14,6 @@
 import type { BrainEngine } from './engine.ts';
 import type { PageType } from './types.ts';
 import { ensureWellFormed } from './text-safe.ts';
-import { slugifyPath } from './sync.ts';
 
 /**
  * v0.42.7 — link-extraction version stamp. Bump this ISO timestamp whenever the
@@ -483,29 +482,14 @@ export async function extractPageLinks(
     // pre-v0.40.8.2 behavior of dropping bare wikilinks outside
     // DIR_PATTERN.
     if (ref.needsResolution) {
-      if (typeof resolver.resolveBasenameMatches !== 'function') continue;
+      if (!opts.globalBasename || typeof resolver.resolveBasenameMatches !== 'function') {
+        continue;
+      }
       // Issue #972 (codex): resolve by the wikilink TARGET (ref.slug — the
       // text inside `[[...]]` before any `|`), NOT the display alias
       // (ref.name = match[2]). `[[struktura|the project]]` must resolve
       // `struktura`, not "the project". The display text is for context only.
-      //
-      // Issue #1964: a dir-qualified wikilink (`[[llm-wiki/entities/AI 3.0]]`)
-      // carries a raw Obsidian path while page slugs are sync-slugified
-      // (`llm-wiki/entities/ai-3.0`). Slugify the path the same way sync does,
-      // then match by exact slug or path-suffix (wiki-root-relative authoring).
-      // This runs regardless of global_basename — it's dir-qualified, so the
-      // cross-dir false-positive risk the flag guards against doesn't apply.
-      // Mirrors the FS path's resolveSlug ancestor walk. Bare `[[name]]`
-      // wikilinks still require the global_basename flag.
-      let matches: string[] = [];
-      const slugified = ref.slug.includes('/') ? slugifyPath(ref.slug) : '';
-      if (slugified.includes('/')) {
-        const tail = slugified.slice(slugified.lastIndexOf('/') + 1);
-        matches = (await resolver.resolveBasenameMatches(tail))
-          .filter(m => m === slugified || m.endsWith(`/${slugified}`));
-      } else if (opts.globalBasename) {
-        matches = await resolver.resolveBasenameMatches(ref.slug);
-      }
+      const matches = await resolver.resolveBasenameMatches(ref.slug);
       if (matches.length === 0) continue;
       const idx = content.indexOf(ref.slug);
       const context = idx >= 0 ? excerpt(content, idx, 240) : ref.name;

test/autopilot-fanout-wiring.test.ts

@@ -54,6 +54,20 @@ 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

@@ -14,6 +14,7 @@ import { describe, test, expect } from 'bun:test';
 import {
   readLastFullCycleAt,
   isSourceStale,
+  countStaleSources,
   selectSourcesForDispatch,
   resolveFanoutMax,
   dispatchPerSource,
@@ -74,6 +75,23 @@ 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

@@ -3,8 +3,10 @@
  * cycles. Closes codex round-1 P0-5 (write site for last_full_cycle_at
  * was unspecified pre-PR).
  *
- * Conditions for write:
- *   - opts.sourceId is set (legacy callers without sourceId skip the write)
+ * 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)
  *   - engine is non-null (no-DB path skips)
  *   - status is 'ok' | 'clean' | 'partial' (failed/skipped don't mark fresh)
  *   - dryRun is false
@@ -90,17 +92,45 @@ describe('runCycle last_full_cycle_at exit hook', () => {
     });
   });
 
-  test('legacy caller (no sourceId) does NOT write any source timestamp', async () => {
+  test('no explicit sourceId but brainDir resolves a source → writes the resolved source timestamp', async () => {
     await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('default-like');
-      // No sourceId passed; should remain untouched.
+      // 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 runCycle(engine, {
         brainDir,
         phases: ['lint'],
       });
-      // No per-source write happens; default source's config stays empty.
-      const after = await readLastFullCycleAt('default-like');
-      expect(after).toBeNull();
+      expect(await readLastFullCycleAt('unmatched')).toBeNull();
     });
   });
 

test/extract-fs.test.ts

@@ -389,33 +389,6 @@ describe('resolveSlugAll', () => {
   });
 });
 
-// ─── issue #1964: cross-directory wikilinks — slug/path mismatch ──────────
-
-describe('issue #1964: raw Obsidian wikilink paths resolve to sync-slugified slugs', () => {
-  test('resolveSlug slugifies the candidate (sync-consistent), no flag needed', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // Wikilink literal `[[llm-wiki/entities/AI 3.0]]` — spaces + uppercase.
-    expect(resolveSlug('llm-wiki/notes', 'llm-wiki/entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('resolveSlug slugifies raw (unslugified) fileDir too', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // fileDir comes from dirname(relPath) — the raw on-disk directory.
-    expect(resolveSlug('LLM Wiki/Notes', 'entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('extractLinksFromFile resolves cross-directory wikilink with flag OFF as a typed edge', async () => {
-    const allSlugs = new Set(['llm-wiki/entities/ai-3.0', 'llm-wiki/notes/roadmap']);
-    const content = '---\ntitle: Roadmap\ntype: concept\n---\n\nSee [[llm-wiki/entities/AI 3.0]].\n';
-    const links = await extractLinksFromFile(content, 'llm-wiki/notes/roadmap.md', allSlugs);
-    expect(links.map(l => l.to_slug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    // Dir-qualified path resolution is exact, NOT the basename fallback.
-    expect(links[0].link_type).not.toBe('wikilink_basename');
-  });
-});
-
 describe('issue #972 repro: bare wikilinks resolve when flag is on', () => {
   // End-to-end: reproduces the issue's exact repro inside a tempdir +
   // PGLite, then asserts edge count under both flag states.

test/link-extraction.test.ts

@@ -9,8 +9,6 @@ import {
   parseTimelineEntries,
   isAutoLinkEnabled,
   FRONTMATTER_LINK_MAP,
-  buildBasenameIndex,
-  queryBasenameIndex,
   type SlugResolver,
 } from '../src/core/link-extraction.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
@@ -426,46 +424,6 @@ describe('extractPageLinks', () => {
     expect(strk!.linkType).toBe('wikilink_basename');
   });
 
-  // ─── issue #1964: dir-qualified wikilinks with raw Obsidian paths ────────
-
-  test('#1964: dir-qualified wikilink resolves via sync-consistent slugification (flag OFF)', async () => {
-    // `[[llm-wiki/entities/AI 3.0]]` is a raw Obsidian path; the page slug
-    // is the sync-slugified `llm-wiki/entities/ai-3.0`. Must resolve WITHOUT
-    // global_basename (it's dir-qualified) and must NOT leak to a same-tail
-    // page in a different directory.
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) =>
-        name === 'ai-3.0' ? ['other/ai-3.0', 'llm-wiki/entities/ai-3.0'] : [],
-    };
-    const { candidates } = await extractPageLinks(
-      'llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]] for the model.',
-      {}, 'concept', resolver,
-      // opts.globalBasename omitted (= false) — path is dir-qualified
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    expect(candidates[0].linkType).toBe('wikilink_basename');
-    expect(candidates[0].linkSource).toBe('wikilink-resolved');
-  });
-
-  test('#1964: path-suffix match resolves wiki-root-relative paths against a real index', async () => {
-    // Author writes `[[llm-wiki/entities/AI 3.0]]` but the brain nests the
-    // wiki under a vault dir. Suffix match rescues it; queried through the
-    // REAL basename index so the tail-key lookup is exercised end to end.
-    const idx = buildBasenameIndex(['vault/llm-wiki/entities/ai-3.0', 'people/ai-3.0']);
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) => queryBasenameIndex(idx, name),
-    };
-    const { candidates } = await extractPageLinks(
-      'vault/llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]].',
-      {}, 'concept', resolver,
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['vault/llm-wiki/entities/ai-3.0']);
-  });
-
   test('opts.skipFrontmatter suppresses the frontmatter pass', async () => {
     // Real resolver shape that WOULD resolve frontmatter source: too,
     // but skipFrontmatter blocks the path entirely.