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.ts

@@ -2,14 +2,14 @@
  * State query handlers — STATE.md loading, field extraction, and snapshots.
  *
  * Ported from get-shit-done/bin/lib/state.cjs and core.cjs.
- * Provides state.load (rebuild frontmatter from body + disk), state.get
+ * Provides `state json` / `state.json` (rebuilt frontmatter JSON, `stateJson`), `state.get`
  * (field/section extraction), and state-snapshot (structured snapshot).
  *
  * @example
  * ```typescript
- * import { stateLoad, stateGet, stateSnapshot } from './state.js';
+ * import { stateJson, stateGet, stateSnapshot } from './state.js';
  *
- * const loaded = await stateLoad([], '/project');
+ * const loaded = await stateJson([], '/project');
  * // { data: { gsd_state_version: '1.0', milestone: 'v3.0', ... } }
  *
  * const field = await stateGet(['Status'], '/project');
@@ -187,7 +187,7 @@ export async function buildStateFrontmatter(bodyContent: string, projectDir: str
 // ─── Exported handlers ─────────────────────────────────────────────────────
 
 /**
- * Query handler for state.load / state.json.
+ * Query handler for `state json` / `state.json` (CJS `cmdStateJson`).
  *
  * Reads STATE.md, rebuilds frontmatter from body + disk scanning.
  * Returns cached frontmatter-only fields (stopped_at, paused_at) when not in body.
@@ -198,7 +198,7 @@ export async function buildStateFrontmatter(bodyContent: string, projectDir: str
  * @param projectDir - Project root directory
  * @returns QueryResult with rebuilt state frontmatter
  */
-export const stateLoad: QueryHandler = async (_args, projectDir) => {
+export const stateJson: QueryHandler = async (_args, projectDir) => {
   const statePath = planningPaths(projectDir).state;
 
   let content: string;
@@ -319,10 +319,12 @@ export const stateSnapshot: QueryHandler = async (_args, projectDir) => {
   // Parse numeric fields
   const totalPhases = totalPhasesRaw ? parseInt(totalPhasesRaw, 10) : null;
   const totalPlansInPhase = totalPlansRaw ? parseInt(totalPlansRaw, 10) : null;
-  const progressPercent = progressRaw ? (() => {
-    const m = progressRaw.match(/(\d+)%/);
-    return m ? parseInt(m[1], 10) : null;
-  })() : null;
+  // Match gsd-tools `cmdStateSnapshot` (state.cjs): parseInt(progressRaw.replace('%',''), 10) — NaN → null
+  let progressPercent: number | null = null;
+  if (progressRaw) {
+    const n = parseInt(progressRaw.replace(/%/g, ''), 10);
+    progressPercent = Number.isFinite(n) ? n : null;
+  }
 
   // Extract decisions table
   const decisions: Array<{ phase: string; summary: string; rationale: string }> = [];