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/detect-custom-files.ts

@@ -0,0 +1,97 @@
+/**
+ * Detect user-added files under GSD-managed install dirs not listed in the manifest.
+ *
+ * Port of `detect-custom-files` from `get-shit-done/bin/gsd-tools.cjs` (lines 1161–1239).
+ */
+
+import { existsSync, readdirSync, readFileSync } from 'node:fs';
+import { join, relative, resolve } from 'node:path';
+
+import type { QueryHandler } from './utils.js';
+
+const GSD_MANAGED_DIRS = [
+  'get-shit-done',
+  'agents',
+  join('commands', 'gsd'),
+  'hooks',
+  'command',
+  'skills',
+];
+
+function walkDir(dir: string, baseDir: string): string[] {
+  const results: string[] = [];
+  if (!existsSync(dir)) return results;
+  for (const entry of readdirSync(dir, { withFileTypes: true })) {
+    const fullPath = join(dir, entry.name);
+    if (entry.isDirectory()) {
+      results.push(...walkDir(fullPath, baseDir));
+    } else {
+      const relPath = relative(baseDir, fullPath).split('\\').join('/');
+      results.push(relPath);
+    }
+  }
+  return results;
+}
+
+/**
+ * Args: `--config-dir <path>` (required) — runtime config directory to scan.
+ */
+export const detectCustomFiles: QueryHandler = async (args) => {
+  const configDirIdx = args.indexOf('--config-dir');
+  const configDir = configDirIdx !== -1 ? args[configDirIdx + 1] : null;
+  if (!configDir) {
+    return { data: { error: 'Usage: detect-custom-files --config-dir <path>' } };
+  }
+
+  const resolvedConfigDir = resolve(configDir);
+  if (!existsSync(resolvedConfigDir)) {
+    return { data: { error: `Config directory not found: ${resolvedConfigDir}` } };
+  }
+
+  const manifestPath = join(resolvedConfigDir, 'gsd-file-manifest.json');
+  if (!existsSync(manifestPath)) {
+    return {
+      data: {
+        custom_files: [] as string[],
+        custom_count: 0,
+        manifest_found: false,
+      },
+    };
+  }
+
+  let manifest: { version?: string; files?: Record<string, unknown> };
+  try {
+    manifest = JSON.parse(readFileSync(manifestPath, 'utf8')) as { version?: string; files?: Record<string, unknown> };
+  } catch {
+    return {
+      data: {
+        custom_files: [] as string[],
+        custom_count: 0,
+        manifest_found: false,
+        error: 'manifest parse error',
+      },
+    };
+  }
+
+  const manifestKeys = new Set(Object.keys(manifest.files || {}));
+
+  const customFiles: string[] = [];
+  for (const managedDir of GSD_MANAGED_DIRS) {
+    const absDir = join(resolvedConfigDir, managedDir);
+    if (!existsSync(absDir)) continue;
+    for (const relPath of walkDir(absDir, resolvedConfigDir)) {
+      if (!manifestKeys.has(relPath)) {
+        customFiles.push(relPath);
+      }
+    }
+  }
+
+  return {
+    data: {
+      custom_files: customFiles,
+      custom_count: customFiles.length,
+      manifest_found: true,
+      manifest_version: manifest.version ?? null,
+    },
+  };
+};