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/config-mutation.ts

@@ -10,7 +10,7 @@
  * import { configSet, configNewProject } from './config-mutation.js';
  *
  * await configSet(['model_profile', 'quality'], '/project');
- * // { data: { set: true, key: 'model_profile', value: 'quality' } }
+ * // { data: { updated: true, key: 'model_profile', value: 'quality', previousValue: 'balanced' } }
  *
  * await configNewProject([], '/project');
  * // { data: { created: true, path: '.planning/config.json' } }
@@ -22,7 +22,7 @@ import { existsSync } from 'node:fs';
 import { homedir } from 'node:os';
 import { join } from 'node:path';
 import { GSDError, ErrorClassification } from '../errors.js';
-import { MODEL_PROFILES, VALID_PROFILES } from './config-query.js';
+import { VALID_PROFILES, getAgentToModelMapForProfile } from './config-query.js';
 import { planningPaths } from './helpers.js';
 import { acquireStateLock, releaseStateLock } from './state-mutation.js';
 import type { QueryHandler } from './utils.js';
@@ -177,6 +177,18 @@ export function parseConfigValue(value: string): unknown {
  * @param dotPath - Dot-notation key path (e.g., 'workflow.auto_advance')
  * @param value - Value to set
  */
+function getValueAtPath(obj: Record<string, unknown>, dotPath: string): unknown {
+  const keys = dotPath.split('.');
+  let current: unknown = obj;
+  for (const key of keys) {
+    if (current === undefined || current === null || typeof current !== 'object') {
+      return undefined;
+    }
+    current = (current as Record<string, unknown>)[key];
+  }
+  return current;
+}
+
 function setConfigValue(obj: Record<string, unknown>, dotPath: string, value: unknown): void {
   const keys = dotPath.split('.');
   let current: Record<string, unknown> = obj;
@@ -200,7 +212,7 @@ function setConfigValue(obj: Record<string, unknown>, dotPath: string, value: un
  *
  * @param args - args[0]=key, args[1]=value
  * @param projectDir - Project root directory
- * @returns QueryResult with { set: true, key, value }
+ * @returns QueryResult matching gsd-tools `config-set` JSON: `{ updated, key, value, previousValue }`
  * @throws GSDError with Validation if key is invalid or args missing
  */
 export const configSet: QueryHandler = async (args, projectDir) => {
@@ -233,6 +245,7 @@ export const configSet: QueryHandler = async (args, projectDir) => {
   // D6: Lock protection for read-modify-write (match CJS config.cjs:296)
   const paths = planningPaths(projectDir);
   const lockPath = await acquireStateLock(paths.config);
+  let previousValue: unknown;
   try {
     let config: Record<string, unknown> = {};
     try {
@@ -242,13 +255,23 @@ export const configSet: QueryHandler = async (args, projectDir) => {
       // Start with empty config if file doesn't exist or is malformed
     }
 
+    previousValue = getValueAtPath(config, keyPath);
     setConfigValue(config, keyPath, parsedValue);
     await atomicWriteConfig(paths.config, config);
   } finally {
     await releaseStateLock(lockPath);
   }
 
-  return { data: { set: true, key: keyPath, value: parsedValue } };
+  // Match CJS JSON: `JSON.stringify` omits keys whose value is `undefined`
+  const data: Record<string, unknown> = {
+    updated: true,
+    key: keyPath,
+    value: parsedValue,
+  };
+  if (previousValue !== undefined) {
+    data.previousValue = previousValue;
+  }
+  return { data };
 };
 
 // ─── configSetModelProfile ────────────────────────────────────────────────
@@ -281,6 +304,7 @@ export const configSetModelProfile: QueryHandler = async (args, projectDir) => {
   // D6: Lock protection for read-modify-write
   const paths = planningPaths(projectDir);
   const lockPath = await acquireStateLock(paths.config);
+  let previousProfile = 'balanced';
   try {
     let config: Record<string, unknown> = {};
     try {
@@ -290,13 +314,24 @@ export const configSetModelProfile: QueryHandler = async (args, projectDir) => {
       // Start with empty config
     }
 
+    const prev =
+      typeof config.model_profile === 'string' ? config.model_profile.toLowerCase().trim() : '';
+    previousProfile = VALID_PROFILES.includes(prev) ? prev : 'balanced';
     config.model_profile = normalized;
     await atomicWriteConfig(paths.config, config);
   } finally {
     await releaseStateLock(lockPath);
   }
 
-  return { data: { set: true, profile: normalized, agents: MODEL_PROFILES } };
+  const agentToModelMap = getAgentToModelMapForProfile(normalized);
+  return {
+    data: {
+      updated: true,
+      profile: normalized,
+      previousProfile,
+      agentToModelMap,
+    },
+  };
 };
 
 // ─── configNewProject ─────────────────────────────────────────────────────