feat(sdk): golden parity harness and query handler CJS alignment (#2302 Track A) (#2341)

* feat(sdk): golden parity harness and query handler CJS alignment (#2302 Track A)

Golden/read-only parity tests and registry alignment, query handler fixes
(check-completion, state-mutation, commit, validate, summary, etc.), and
WAITING.json dual-write for .gsd/.planning readers.

Refs gsd-build/get-shit-done#2341

* fix(sdk): getMilestoneInfo matches GSD ROADMAP (🟡, last bold, STATE fallback)

- Recognize in-flight 🟡 milestone bullets like 🚧.
- Derive from last **vX.Y Title** before ## Phases when emoji absent.
- Fall back to STATE.md milestone when ROADMAP is missing; use last bare vX.Y
  in cleaned text instead of first (avoids v1.0 from shipped list).
- Fixes init.execute-phase milestone_version and buildStateFrontmatter after
  state.begin-phase (syncStateFrontmatter).

* feat(sdk): phase list, plan task structure, requirements extract handlers

- Register phase.list-plans, phase.list-artifacts, plan.task-structure,
  requirements.extract-from-plans (SDK-only; golden-policy exceptions).
- Add unit tests; document in QUERY-HANDLERS.md.
- writeProfile: honor --output, render dimensions, return profile_path and dimensions_scored.

* feat(sdk): centralize getGsdAgentsDir in query helpers

Extract agent directory resolution to helpers (GSD_AGENTS_DIR, primary
~/.claude/agents, legacy path). Use from init and docs-init init bundles.

docs(15): add 15-CONTEXT for autonomous phase-15 run.

* feat(sdk): query CLI CJS fallback and session correlation

- createRegistry(eventStream, sessionId) threads correlation into mutation events
- gsd-sdk query falls back to gsd-tools.cjs when no native handler matches
  (disable with GSD_QUERY_FALLBACK=off); stderr bridge warnings
- Export createRegistry from @gsd-build/sdk; add sdk/README.md
- Update QUERY-HANDLERS.md and registry module docs for fallback + sessionId
- Agents: prefer node dist/cli.js query over cat/grep for STATE and plans

* fix(sdk): init phase_found parity, docs-init agents path, state field extract

- Normalize findPhase not-found to null before roadmap fallback (matches findPhaseInternal)

- docs-init: use detectRuntime + resolveAgentsDir for checkAgentsInstalled

- state.cjs stateExtractField: horizontal whitespace only after colon (YAML progress guard)

- Tests: commit_docs default true; config-get golden uses temp config; golden integration green

Refs: #2302

* refactor(sdk): share SessionJsonlRecord in profile-extract-messages

CodeRabbit nit: dedupe JSONL record shape for isGenuineUserMessage and streamExtractMessages.

* fix(sdk): address CodeRabbit major threads (paths, gates, audit, verify)

- Resolve @file: and CLI JSON indirection relative to projectDir; guard empty normalized query command

- plan.task-structure + intel extract/patch-meta: resolvePathUnderProject containment

- check.config-gates: safe string booleans; plan_checker alias precedence over plan_check default

- state.validate/sync: phaseTokenMatches + comparePhaseNum ordering

- verify.schema-drift: token match phase dirs; files_modified from parsed frontmatter

- audit-open: has_scan_errors, unreadable rows, human report when scans fail

- requirements PLANNED key PLAN for root PLAN.md; gsd-tools timeout note

- ingest-docs: repo-root path containment; classifier output slug-hash

Golden parity test strips has_scan_errors until CJS adds field.

* fix: Resolve CodeRabbit security and quality findings
- Secure intel.ts and cli.ts against path traversal
- Catch and validate git add status in commit.ts
- Expand roadmap milestone marker extraction
- Fix parsing array-of-objects in frontmatter YAML
- Fix unhandled config evaluations
- Improve coverage test parity mapping

* test: raise planner character extraction limit to 48K

* fix(sdk): resolve TS build error in docs-init passing config

sdk/src/query/state-mutation.test.ts

@@ -223,14 +223,14 @@ describe('stateUpdate', () => {
 
   it('updates a single field and round-trips through stateLoad', async () => {
     const { stateUpdate } = await import('./state-mutation.js');
-    const { stateLoad } = await import('./state.js');
+    const { stateJson } = await import('./state.js');
 
     const result = await stateUpdate(['Status', 'Phase complete'], tmpDir);
     const data = result.data as Record<string, unknown>;
     expect(data.updated).toBe(true);
 
     // Verify round-trip
-    const loaded = await stateLoad([], tmpDir);
+    const loaded = await stateJson([], tmpDir);
     const loadedData = loaded.data as Record<string, unknown>;
     // Status gets normalized by buildStateFrontmatter
     expect(loadedData.status).toBeTruthy();
@@ -271,7 +271,7 @@ describe('statePatch', () => {
     const patches = JSON.stringify({ Status: 'done', Progress: '100%' });
     const result = await statePatch([patches], tmpDir);
     const data = result.data as Record<string, unknown>;
-    expect(data.patched).toBe(true);
+    expect((data.updated as string[]).length).toBeGreaterThan(0);
 
     // Verify file was updated
     const content = await readFile(join(tmpDir, '.planning', 'STATE.md'), 'utf-8');
@@ -319,7 +319,7 @@ describe('stateBeginPhase', () => {
     // Must return the actual values, not the flag names
     expect(data.phase).toBe('99');
     expect(data.name).toBe('probe-test');
-    expect(data.plan_count).toBe('1');
+    expect(data.plan_count).toBe(1);
 
     // STATE.md must contain clean output, not literal "--phase"
     const content = await readFile(join(tmpDir, '.planning', 'STATE.md'), 'utf-8');
@@ -337,7 +337,7 @@ describe('stateBeginPhase', () => {
     const data = result.data as Record<string, unknown>;
     expect(data.phase).toBe('42');
     expect(data.name).toBe('Positional Test');
-    expect(data.plan_count).toBe('5');
+    expect(data.plan_count).toBe(5);
   });
 
   it('bug-2420: flag parser throws when a flag value is missing (next token is a flag)', async () => {
@@ -348,6 +348,19 @@ describe('stateBeginPhase', () => {
       stateBeginPhase(['--phase', '--name', 'Title', '--plans', '1'], tmpDir)
     ).rejects.toThrow('missing value for --phase');
   });
+
+  it('does not treat argv after named flags as positional name/plans', async () => {
+    const { stateBeginPhase } = await import('./state-mutation.js');
+
+    const result = await stateBeginPhase(['--phase', '2', '--plans', '3'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.phase).toBe('2');
+    expect(data.phase_name).toBeFalsy();
+    expect(data.plan_count).toBe(3);
+
+    const content = await readFile(join(tmpDir, '.planning', 'STATE.md'), 'utf-8');
+    expect(content).toContain('Plan: 1 of 3');
+  });
 });
 
 // ─── stateAdvancePlan ───────────────────────────────────────────────────────
@@ -391,7 +404,10 @@ describe('stateAddDecision', () => {
   it('appends decision and removes placeholder', async () => {
     const { stateAddDecision } = await import('./state-mutation.js');
 
-    const result = await stateAddDecision(['[Phase 10]: Use lockfile atomicity'], tmpDir);
+    const result = await stateAddDecision(
+      ['--phase', '10', '--summary', 'Use lockfile atomicity'],
+      tmpDir,
+    );
     const data = result.data as Record<string, unknown>;
     expect(data.added).toBe(true);
 
@@ -422,8 +438,8 @@ describe('stateRecordSession', () => {
     const { stateRecordSession } = await import('./state-mutation.js');
 
     const result = await stateRecordSession(
-      ['2026-04-08T12:00:00Z', 'Completed 11-01-PLAN.md'],
-      tmpDir
+      ['--stopped-at', 'Completed 11-01-PLAN.md', '--resume-file', 'None'],
+      tmpDir,
     );
     const data = result.data as Record<string, unknown>;
     expect(data.recorded).toBe(true);