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/frontmatter-mutation.ts

@@ -164,9 +164,25 @@ function parseSimpleValue(value: string): unknown {
  * @returns QueryResult with { updated: true, field, value }
  */
 export const frontmatterSet: QueryHandler = async (args, projectDir) => {
-  const filePath = args[0];
-  const field = args[1];
-  const value = args[2];
+  let filePath: string;
+  let field: string;
+  let value: string;
+
+  const fi = args.indexOf('--field');
+  const vi = args.indexOf('--value');
+  const hasNamedArgs = fi !== -1 || vi !== -1;
+  if (hasNamedArgs) {
+    if (fi === -1 || vi === -1 || !args[fi + 1] || args[vi + 1] === undefined) {
+      throw new GSDError('file, --field, and --value required together', ErrorClassification.Validation);
+    }
+    filePath = args[0];
+    field = args[fi + 1];
+    value = args[vi + 1];
+  } else {
+    filePath = args[0];
+    field = args[1];
+    value = args[2];
+  }
 
   if (!filePath || !field || value === undefined) {
     throw new GSDError('file, field, and value required', ErrorClassification.Validation);
@@ -195,11 +211,12 @@ export const frontmatterSet: QueryHandler = async (args, projectDir) => {
   }
 
   const fm = extractFrontmatter(content);
-  fm[field] = parseSimpleValue(value);
+  const parsedValue = parseSimpleValue(value);
+  fm[field] = parsedValue;
   const newContent = spliceFrontmatter(content, fm);
   await writeFile(fullPath, normalizeMd(newContent), 'utf-8');
 
-  return { data: { updated: true, field, value: fm[field] } };
+  return { data: { updated: true, field, value: parsedValue } };
 };
 
 // ─── frontmatterMerge ──────────────────────────────────────────────────────
@@ -210,13 +227,14 @@ export const frontmatterSet: QueryHandler = async (args, projectDir) => {
  * Reads a file, merges JSON object into existing frontmatter, writes back.
  * Port of `cmdFrontmatterMerge` from frontmatter.cjs lines 344-356.
  *
- * @param args - args[0]: file path, args[1]: JSON string
+ * @param args - `file --data <json>` (gsd-tools) or `[file, jsonString]` (SDK)
  * @param projectDir - Project root directory
  * @returns QueryResult with { merged: true, fields: [...] }
  */
 export const frontmatterMerge: QueryHandler = async (args, projectDir) => {
   const filePath = args[0];
-  const jsonString = args[1];
+  const dataIdx = args.indexOf('--data');
+  const jsonString = dataIdx !== -1 ? args[dataIdx + 1] : args[1];
 
   if (!filePath || !jsonString) {
     throw new GSDError('file and data required', ErrorClassification.Validation);