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/config.ts

@@ -23,6 +23,8 @@ export interface WorkflowConfig {
   plan_check: boolean;
   verifier: boolean;
   nyquist_validation: boolean;
+  /** Mirrors gsd-tools flat `config.tdd_mode` (from `workflow.tdd_mode`). */
+  tdd_mode: boolean;
   auto_advance: boolean;
   node_repair: boolean;
   node_repair_budget: number;
@@ -34,6 +36,8 @@ export interface WorkflowConfig {
   skip_discuss: boolean;
   /** Maximum self-discuss passes in auto/headless mode before forcing proceed. Default: 3. */
   max_discuss_passes: number;
+  /** Subagent timeout in ms (matches `get-shit-done/bin/lib/core.cjs` default 300000). */
+  subagent_timeout: number;
 }
 
 export interface HooksConfig {
@@ -52,6 +56,12 @@ export interface GSDConfig {
   workflow: WorkflowConfig;
   hooks: HooksConfig;
   agent_skills: Record<string, unknown>;
+  /** Project slug for branch templates; mirrors gsd-tools `config.project_code`. */
+  project_code?: string | null;
+  /** Interactive vs headless; mirrors gsd-tools flat `config.mode`. */
+  mode?: string;
+  /** Internal auto-chain flag; mirrors gsd-tools `config._auto_chain_active`. */
+  _auto_chain_active?: boolean;
   [key: string]: unknown;
 }
 
@@ -76,6 +86,7 @@ export const CONFIG_DEFAULTS: GSDConfig = {
     plan_check: true,
     verifier: true,
     nyquist_validation: true,
+    tdd_mode: false,
     auto_advance: false,
     node_repair: true,
     node_repair_budget: 2,
@@ -86,11 +97,15 @@ export const CONFIG_DEFAULTS: GSDConfig = {
     discuss_mode: 'discuss',
     skip_discuss: false,
     max_discuss_passes: 3,
+    subagent_timeout: 300000,
   },
   hooks: {
     context_warnings: true,
   },
   agent_skills: {},
+  project_code: null,
+  mode: 'interactive',
+  _auto_chain_active: false,
 };
 
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