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

@@ -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/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;

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-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.

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);