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/plan-task-structure.test.ts

@@ -0,0 +1,65 @@
+/**
+ * Unit tests for plan.task-structure.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtemp, writeFile, mkdir, rm } from 'node:fs/promises';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { planTaskStructure } from './plan-task-structure.js';
+
+const PLAN = `---
+phase: 09-foundation
+plan: "01"
+wave: 2
+depends_on: []
+autonomous: false
+---
+
+<objective>
+Test objective
+</objective>
+
+<tasks>
+<task type="auto">
+  <name>First</name>
+</task>
+<task type="checkpoint">
+  <name>Gate</name>
+</task>
+</tasks>
+`;
+
+let tmpDir: string;
+let planPath: string;
+
+beforeEach(async () => {
+  tmpDir = await mkdtemp(join(tmpdir(), 'gsd-pts-'));
+  const rel = join('.planning', 'phases', '09-x', '09-01-PLAN.md');
+  planPath = join(tmpDir, rel);
+  await mkdir(join(tmpDir, '.planning', 'phases', '09-x'), { recursive: true });
+  await writeFile(planPath, PLAN);
+});
+
+afterEach(async () => {
+  await rm(tmpDir, { recursive: true, force: true });
+});
+
+describe('planTaskStructure', () => {
+  it('returns wave, tasks, and checkpoints', async () => {
+    const rel = join('.planning', 'phases', '09-x', '09-01-PLAN.md');
+    const r = await planTaskStructure([rel], tmpDir);
+    const d = r.data as {
+      wave: number;
+      autonomous: boolean;
+      task_count: number;
+      checkpoint_count: number;
+      tasks: Array<{ is_checkpoint: boolean }>;
+    };
+    expect(d.wave).toBe(2);
+    expect(d.autonomous).toBe(false);
+    expect(d.task_count).toBe(2);
+    expect(d.checkpoint_count).toBe(1);
+    expect(d.tasks.filter((t) => t.is_checkpoint).length).toBe(1);
+  });
+});