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/check-auto-mode.ts

@@ -0,0 +1,50 @@
+/**
+ * Consolidated auto-advance flags (`check.auto-mode`).
+ *
+ * Replaces paired `config-get workflow.auto_advance` + `config-get workflow._auto_chain_active`
+ * for checkpoint and auto-advance gates. See `.planning/research/decision-routing-audit.md` §3.5.
+ *
+ * Semantics match `execute-phase.md`: automation applies when **either** the ephemeral chain flag
+ * or the persistent user preference is true (`active === true`).
+ */
+
+import { CONFIG_DEFAULTS, loadConfig } from '../config.js';
+import type { QueryHandler } from './utils.js';
+
+export type AutoModeSource = 'auto_chain' | 'auto_advance' | 'both' | 'none';
+
+function resolveSource(
+  autoChainActive: boolean,
+  autoAdvance: boolean,
+): { active: boolean; source: AutoModeSource } {
+  if (autoChainActive && autoAdvance) {
+    return { active: true, source: 'both' };
+  }
+  if (autoChainActive) {
+    return { active: true, source: 'auto_chain' };
+  }
+  if (autoAdvance) {
+    return { active: true, source: 'auto_advance' };
+  }
+  return { active: false, source: 'none' };
+}
+
+export const checkAutoMode: QueryHandler = async (_args, projectDir) => {
+  const config = await loadConfig(projectDir);
+  const wf: Record<string, unknown> = {
+    ...CONFIG_DEFAULTS.workflow,
+    ...(config.workflow as unknown as Record<string, unknown>),
+  };
+  const autoAdvance = Boolean(wf.auto_advance ?? false);
+  const autoChainActive = Boolean(wf._auto_chain_active ?? false);
+  const { active, source } = resolveSource(autoChainActive, autoAdvance);
+
+  return {
+    data: {
+      active,
+      source,
+      auto_chain_active: autoChainActive,
+      auto_advance: autoAdvance,
+    },
+  };
+};