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/cli.ts

@@ -24,7 +24,6 @@ import type { GBrainConfig } from './core/config.ts';
 import type { AIGatewayConfig } from './core/ai/types.ts';
 import type { BrainEngine } from './core/engine.ts';
 import { operations, OperationError } from './core/operations.ts';
-import { resolveSourceIdEngineFree } from './core/source-resolver.ts';
 import { formatVolunteeredPage } from './core/context/volunteer.ts';
 import type { Operation, OperationContext } from './core/operations.ts';
 import { shouldForceExitAfterMain, finishCliTeardown, flushThenExit, currentExitCode, setCliExitVerdict } from './core/cli-force-exit.ts';
@@ -383,15 +382,6 @@ async function main() {
     if (op.localOnly) {
       refuseThinClient(command, cfgPre!.remote_mcp!.mcp_url);
     }
-    // #2098: the local path resolves --source / GBRAIN_SOURCE / .gbrain-source
-    // inside makeContext (ctx.sourceId), which this route never reaches — so
-    // scope must be mapped onto the op's source_id wire param before the call.
-    try {
-      applyThinClientSourceScope(op, params);
-    } catch (e: unknown) {
-      console.error(e instanceof Error ? e.message : String(e));
-      process.exit(1);
-    }
     await runThinClientRouted(op, params, cfgPre!, cliOpts);
     return;
   }
@@ -812,60 +802,6 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
   return params;
 }
 
-/**
- * #2098: thin-client source scoping. Locally, --source / GBRAIN_SOURCE /
- * .gbrain-source resolve to ctx.sourceId in makeContext; the thin-client
- * route short-circuits before that, so `gbrain query --source X` against a
- * remote brain silently searched unscoped. This runs the engine-free tiers
- * (flag → env → dotfile; the DB-backed tiers can't run without an engine —
- * the server's grant scoping covers the rest) and maps the result onto the
- * op's `source_id` wire param.
- *
- * Ops that declare their OWN `source` param (facts add, etc.) are left
- * untouched — their --source is an op param, not scope. An explicit --source
- * on an op with no source_id wire param throws (loud beats silent drop);
- * ambient env/dotfile scope with nowhere to send it is ignored, matching the
- * pre-fix behavior for non-scopeable ops. Exported for tests.
- */
-// Ops whose `source_id` wire param is NOT read-scope semantics: get_skill's
-// source_id flips the lookup from host catalog to brain-resident-pack
-// (getResidentSkillDetail). Ambient env/dotfile scope must never leak into
-// these; an explicit --source-id still passes through untouched above.
-const NON_SCOPE_SOURCE_ID_OPS = new Set(['get_skill']);
-
-export function applyThinClientSourceScope(
-  op: Operation,
-  params: Record<string, unknown>,
-  cwd?: string,
-): void {
-  if ('source' in op.params) return; // the op owns --source; not a scope flag
-  const explicit = typeof params.source === 'string' && params.source.length > 0
-    ? (params.source as string)
-    : null;
-  delete params.source; // never a wire param on these ops — don't leak it
-  // Explicit per-call scope already on the wire wins over ambient tiers.
-  if (params.source_id !== undefined || params.all_sources === true) {
-    if (explicit) {
-      throw new Error('Pass either --source or --source-id/--all-sources, not both.');
-    }
-    return;
-  }
-  const resolved = resolveSourceIdEngineFree(explicit, cwd);
-  if (!resolved) return;
-  if (!('source_id' in op.params) || NON_SCOPE_SOURCE_ID_OPS.has(op.name)) {
-    if (explicit) {
-      const hint = NON_SCOPE_SOURCE_ID_OPS.has(op.name)
-        ? `(its source_id parameter is not a scope filter; pass --source-id explicitly if you mean it)`
-        : `(the remote op has no source_id parameter; the server scopes it to your grant)`;
-      throw new Error(
-        `gbrain ${op.cliHints?.name || op.name} does not accept --source on a thin-client install ${hint}.`,
-      );
-    }
-    return; // ambient env/dotfile scope with nowhere to send it
-  }
-  params.source_id = resolved;
-}
-
 async function makeContext(engine: BrainEngine, params: Record<string, unknown>): Promise<OperationContext> {
   // v0.31.8 (D11): resolve sourceId via the canonical 6-tier chain. Honors
   // --source / GBRAIN_SOURCE / .gbrain-source / path-match / brain default /

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;
 }
 
 /**

src/core/source-resolver.ts

@@ -160,33 +160,6 @@ export async function resolveSourceId(
   return 'default';
 }
 
-/**
- * Engine-free tiers (1-3) of the resolution chain: explicit flag →
- * GBRAIN_SOURCE env → .gbrain-source dotfile walk. Used by the thin-client
- * CLI path (#2098), which has no local engine to run tiers 4-6 or
- * assertSourceExists against — the remote server enforces existence + grant.
- * Returns null when no engine-free tier fires.
- */
-export function resolveSourceIdEngineFree(
-  explicit: string | null | undefined,
-  cwd: string = process.cwd(),
-): string | null {
-  if (explicit) {
-    if (!SOURCE_ID_RE.test(explicit)) {
-      throw new Error(`Invalid --source value "${explicit}". Must match [a-z0-9-]{1,32}.`);
-    }
-    return explicit;
-  }
-  const env = process.env.GBRAIN_SOURCE;
-  if (env && env.length > 0) {
-    if (!SOURCE_ID_RE.test(env)) {
-      throw new Error(`Invalid GBRAIN_SOURCE value "${env}". Must match [a-z0-9-]{1,32}.`);
-    }
-    return env;
-  }
-  return readDotfileWalk(cwd);
-}
-
 /**
  * Returns the id of the SINGLE registered non-default source with a
  * local_path, when exactly one such row exists. Returns null when:

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/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);

test/thin-client-source-scope.test.ts

@@ -1,142 +0,0 @@
-/**
- * #2098: thin-client routing dropped --source / GBRAIN_SOURCE / .gbrain-source.
- *
- * The local CLI path resolves source scope in makeContext (ctx.sourceId); the
- * thin-client route short-circuits before that and sent params verbatim, so
- * `gbrain query --source X` against a remote brain silently searched unscoped
- * (the server op ignores the unknown `source` key).
- *
- * applyThinClientSourceScope runs the engine-free tiers (flag → env → dotfile)
- * and maps the result onto the op's `source_id` wire param. These tests fail
- * without the fix (params.source_id stays undefined / params.source leaks).
- */
-
-import { describe, test, expect } from 'bun:test';
-import { mkdtempSync, rmSync, writeFileSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import { applyThinClientSourceScope, parseOpArgs } from '../src/cli.ts';
-import { operationsByName } from '../src/core/operations.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-const queryOp = operationsByName.query;
-
-describe('applyThinClientSourceScope (#2098)', () => {
-  test('--source maps onto the query op wire param source_id', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['find things', '--source', 'wiki']);
-      expect(params.source).toBe('wiki'); // pre-fix state: wrong key
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBe('wiki');
-      expect('source' in params).toBe(false); // never leaks the unknown key
-    });
-  });
-
-  test('GBRAIN_SOURCE env tier fires when no flag is passed', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
-      const params = parseOpArgs(queryOp, ['find things']);
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBe('gstack');
-    });
-  });
-
-  test('.gbrain-source dotfile tier fires when flag and env are absent', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const tmp = mkdtempSync(join(tmpdir(), 'gbrain-thin-scope-'));
-      try {
-        writeFileSync(join(tmp, '.gbrain-source'), 'essays\n');
-        const params = parseOpArgs(queryOp, ['find things']);
-        applyThinClientSourceScope(queryOp, params, tmp);
-        expect(params.source_id).toBe('essays');
-      } finally {
-        rmSync(tmp, { recursive: true, force: true });
-      }
-    });
-  });
-
-  test('explicit --source-id on the wire wins over ambient env scope', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
-      const params = parseOpArgs(queryOp, ['find things', '--source-id', 'wiki']);
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBe('wiki');
-    });
-  });
-
-  test('--source together with --source-id is rejected loudly', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['q', '--source', 'a', '--source-id', 'b']);
-      expect(() => applyThinClientSourceScope(queryOp, params, '/')).toThrow(/not both/);
-    });
-  });
-
-  test('invalid --source value is rejected loudly', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['q', '--source', 'Bad_Value!']);
-      expect(() => applyThinClientSourceScope(queryOp, params, '/')).toThrow(/Invalid --source/);
-    });
-  });
-
-  test('--source on an op with no source_id wire param errors instead of silently dropping', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const op = operationsByName.add_tag;
-      expect('source_id' in op.params).toBe(false);
-      const params = { slug: 'x', tag: 'y', source: 'wiki' };
-      expect(() => applyThinClientSourceScope(op, params, '/')).toThrow(/--source/);
-    });
-  });
-
-  test('ambient env scope on an op with no source_id wire param is ignored (no throw)', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'wiki' }, () => {
-      const op = operationsByName.add_tag;
-      const params: Record<string, unknown> = { slug: 'x', tag: 'y' };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source_id).toBeUndefined();
-    });
-  });
-
-  test('ops that declare their OWN source param are left untouched', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const op = operationsByName.put_raw_data;
-      expect('source' in op.params).toBe(true);
-      const params: Record<string, unknown> = { slug: 'x', source: 'crustdata', data: {} };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source).toBe('crustdata');
-      expect(params.source_id).toBeUndefined();
-    });
-  });
-
-  test('get_skill: ambient scope never leaks into its non-scope source_id param', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'wiki' }, () => {
-      const op = operationsByName.get_skill;
-      expect('source_id' in op.params).toBe(true); // has the param, but it is a mode switch
-      const params: Record<string, unknown> = { name: 'ingest' };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source_id).toBeUndefined(); // would flip host catalog → brain-pack lookup
-    });
-  });
-
-  test('get_skill: explicit --source errors instead of masquerading as --source-id', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const op = operationsByName.get_skill;
-      const params: Record<string, unknown> = { name: 'ingest', source: 'wiki' };
-      expect(() => applyThinClientSourceScope(op, params, '/')).toThrow(/--source-id/);
-    });
-  });
-
-  test('get_skill: explicit --source-id passes through untouched', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
-      const op = operationsByName.get_skill;
-      const params: Record<string, unknown> = { name: 'ingest', source_id: 'wiki' };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source_id).toBe('wiki');
-    });
-  });
-
-  test('no scope from any tier leaves params unchanged', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['find things']);
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBeUndefined();
-    });
-  });
-});