fix(skillopt): emit proposed.md in no-mutate mode (#2635)

writeProposed now writes both best.md (optimizer's current-best pointer)
and proposed.md (the stable review artifact documented by --no-mutate);
the orchestrator returns the real proposed.md path instead of aliasing
best.md. Fix lands in the shared helper so both accept-branch call sites
are covered.

Takeover of #2719.

Co-authored-by: RerankerGuo <RerankerGuo@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/tutorials/improving-skills-with-skillopt.md

@@ -233,13 +233,14 @@ keep it or `git checkout` to throw it away. Nothing is committed for you.
 
 **For a skill that ships with gbrain** (anything under the gbrain repo's own
 `skills/`): SkillOpt refuses to overwrite it by default and writes the winner to
-`skills/<name>/skillopt/best.md` instead, so an optimization pass can never
-silently mutate a skill other people depend on. Two ways to handle that:
+`skills/<name>/skillopt/proposed.md` instead (while keeping `best.md` as the
+optimizer's current-best pointer), so an optimization pass can never silently
+mutate a skill other people depend on. Two ways to handle that:
 
 ```bash
 # See the proposed improvement without touching SKILL.md (works for ANY skill):
 gbrain skillopt meeting-prep --split 1:1:1 --no-mutate
-# → writes skills/meeting-prep/skillopt/best.md (the proposed rewrite), prints its path. Copy what you want.
+# → writes skills/meeting-prep/skillopt/proposed.md, updates best.md, and prints the proposal path.
 
 # Actually rewrite a bundled skill (explicit opt-in + an independent held-out set):
 gbrain skillopt brain-ops --split 1:1:1 --allow-mutate-bundled \

src/commands/extract.ts

@@ -1743,15 +1743,7 @@ 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.
-      //
-      // 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 });
+      processedRefs.push({ slug: page.slug, source_id: page.source_id, extractedAt: page.updated_at_iso });
     }
 
     // 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 = '2026-07-21T00:00:00Z';
+export const LINK_EXTRACTOR_VERSION_TS = '2026-05-31T00:00:00Z';
 
 // ─── 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, ops (domain-organized wikis)
+ *   - Our domain extensions: tech, finance, personal, openclaw (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|ops)';
+const DIR_PATTERN = '(?:people|companies|meetings|concepts|deal|civic|project|projects|source|media|yc|tech|finance|personal|openclaw|entities)';
 
 /**
  * Match `[Name](path)` markdown links pointing to entity directories.
@@ -865,16 +865,7 @@ export function queryBasenameIndex(idx: Map<string, string[]>, name: string): st
   if (!name || typeof name !== 'string') return [];
   const trimmed = name.trim();
   if (!trimmed) return [];
-  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));
-  }
+  const hit = idx.get(trimmed) ?? idx.get(trimmed.toLowerCase()) ?? idx.get(normalizeBasename(trimmed));
   return hit ? [...hit].sort(basenameSort) : [];
 }
 

src/core/skillopt/orchestrator.ts

@@ -93,7 +93,13 @@ import { resolveLrSchedule } from './lr-schedule.ts';
 import { preflight, formatPreflightReport } from './preflight.ts';
 import { isRejected, loadRejectedBuffer, makeRejectedEntry, saveRejectedBuffer } from './rejected-buffer.ts';
 import { runReflect, runOneShotRewrite, describeJudges } from './reflect.ts';
-import { acceptCandidate, bestPath, revertAllPending, skillPath, writeProposed } from './version-store.ts';
+import {
+  acceptCandidate,
+  proposedPath as proposedFilePath,
+  revertAllPending,
+  skillPath,
+  writeProposed,
+} from './version-store.ts';
 import { runValidationGate, scoreSkillOnTasks } from './validate-gate.ts';
 import { ROLLOUT_SUCCESS_THRESHOLD } from './types.ts';
 import type { SkillOptOpts, EditOp, RunReceipt, BenchmarkTask } from './types.ts';
@@ -702,9 +708,9 @@ async function runOptimizationLoop(
   // to the catch's assignment values only (it can't prove the async callback ran).
   const finalOutcome = outcome as 'accepted' | 'no_improvement' | 'aborted' | 'errored';
   if (!mutateDecision.mutate && finalOutcome === 'accepted') {
-    // best.md was written by writeProposed() in the accept branch (no-mutate
-    // path); it doubles as proposed.md for human review. SKILL.md untouched.
-    proposedPath = bestPath(skillsDir, skillName);
+    // writeProposed() emitted both the best pointer and the stable review
+    // artifact in the accept branch. SKILL.md remains untouched.
+    proposedPath = proposedFilePath(skillsDir, skillName);
   } else if (mutateDecision.mutate) {
     mutatedSkillFile = finalOutcome === 'accepted';
   }

src/core/skillopt/version-store.ts

@@ -23,6 +23,7 @@
  *
  *   history.json
  *   best.md
+ *   proposed.md
  *   versions/
  *     v0001_e1_s1.md
  *     v0002_e1_s2.md
@@ -52,6 +53,10 @@ export function bestPath(skillsDir: string, skillName: string): string {
   return path.join(skilloptDir(skillsDir, skillName), 'best.md');
 }
 
+export function proposedPath(skillsDir: string, skillName: string): string {
+  return path.join(skilloptDir(skillsDir, skillName), 'proposed.md');
+}
+
 export function skillPath(skillsDir: string, skillName: string): string {
   return path.join(skillsDir, skillName, 'SKILL.md');
 }
@@ -171,17 +176,18 @@ export function acceptCandidate(input: AcceptInput): AcceptResult {
 }
 
 /**
- * Write the candidate to `best.md` (which doubles as `proposed.md`) WITHOUT
- * touching SKILL.md or the history ledger. Used by the `--no-mutate` /
- * bundled-without-allow paths: the optimizer found a better candidate but the
- * caller opted out of in-place mutation, so we surface it for human review.
- * Returns the path written. Atomic (.tmp + rename).
+ * Write the candidate to both `best.md` and `proposed.md` WITHOUT touching
+ * SKILL.md or the history ledger. `best.md` remains the optimizer's current
+ * best pointer; `proposed.md` is the stable human-review artifact promised by
+ * `--no-mutate`. Returns the proposal path. Each write is atomic (.tmp + rename).
  */
 export function writeProposed(skillsDir: string, skillName: string, candidateText: string): string {
-  const p = bestPath(skillsDir, skillName);
-  fs.mkdirSync(path.dirname(p), { recursive: true });
-  atomicWrite(p, candidateText);
-  return p;
+  const best = bestPath(skillsDir, skillName);
+  const proposed = proposedPath(skillsDir, skillName);
+  fs.mkdirSync(path.dirname(best), { recursive: true });
+  atomicWrite(best, candidateText);
+  atomicWrite(proposed, candidateText);
+  return proposed;
 }
 
 /**

test/e2e/skillopt-loop.serial.test.ts

@@ -39,6 +39,7 @@ import { runSkillOpt } from '../../src/core/skillopt/orchestrator.ts';
 import {
   bestPath,
   loadHistory,
+  proposedPath,
   skillPath,
 } from '../../src/core/skillopt/version-store.ts';
 import { loadRejectedBuffer } from '../../src/core/skillopt/rejected-buffer.ts';
@@ -741,7 +742,7 @@ describe('skillopt T3 — F11 held-out gate, ablation opts, no-DB-pollution', ()
     } finally { fixture.cleanup(); }
   });
 
-  test('--no-mutate writes proposed.md (best.md), leaves SKILL.md untouched', async () => {
+  test('--no-mutate writes proposed.md and best.md, leaves SKILL.md untouched', async () => {
     const fixture = setupFixture(SKILL_PEOPLE_ONLY, CITATIONS_BENCHMARK);
     try {
       installStub({
@@ -753,10 +754,9 @@ describe('skillopt T3 — F11 held-out gate, ablation opts, no-DB-pollution', ()
           const result = await runOnce(fixture, { noMutate: true });
           expect(result.outcome).toBe('accepted');
           expect(result.mutatedSkillFile).toBe(false);
-          expect(result.proposedPath).toBeDefined();
-          // proposed.md (best.md) exists and carries the improvement.
-          expect(fs.existsSync(result.proposedPath!)).toBe(true);
+          expect(result.proposedPath).toBe(proposedPath(fixture.skillsDir, SKILL));
           expect(fs.readFileSync(result.proposedPath!, 'utf8')).toContain('## Citations');
+          expect(fs.readFileSync(bestPath(fixture.skillsDir, SKILL), 'utf8')).toContain('## Citations');
           // SKILL.md on disk is UNCHANGED (still People-only).
           const skill = fs.readFileSync(skillPath(fixture.skillsDir, SKILL), 'utf8');
           expect(skill).not.toContain('## Citations');

test/extract-stale.test.ts

@@ -209,24 +209,6 @@ 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

@@ -140,15 +140,6 @@ 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
@@ -1078,15 +1069,6 @@ 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);

test/skillopt/version-store.test.ts

@@ -12,9 +12,11 @@ import {
   bestPath,
   historyPath,
   loadHistory,
+  proposedPath,
   revertAllPending,
   skillPath,
   versionsDir,
+  writeProposed,
 } from '../../src/core/skillopt/version-store.ts';
 
 let tmpDir: string;
@@ -79,6 +81,19 @@ describe('acceptCandidate (D8 two-phase commit)', () => {
   });
 });
 
+describe('writeProposed', () => {
+  test('writes distinct best and proposed artifacts without mutating SKILL.md (#2635)', () => {
+    const candidate = '---\nname: test\n---\nproposed body\n';
+
+    const written = writeProposed(tmpDir, SKILL, candidate);
+
+    expect(written).toBe(proposedPath(tmpDir, SKILL));
+    expect(fs.readFileSync(bestPath(tmpDir, SKILL), 'utf8')).toBe(candidate);
+    expect(fs.readFileSync(proposedPath(tmpDir, SKILL), 'utf8')).toBe(candidate);
+    expect(fs.readFileSync(skillPath(tmpDir, SKILL), 'utf8')).toContain('baseline body');
+  });
+});
+
 describe('revertAllPending (D8 crash recovery)', () => {
   test('no-op when no pending rows', () => {
     const reverted = revertAllPending(tmpDir, SKILL);