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

agents/gsd-doc-classifier.md

@@ -110,7 +110,7 @@ Regardless of type, extract:
 </step>
 
 <step name="write_output">
-Write to `{OUTPUT_DIR}/{slug}.json` where `slug` is the filename without extension (replace non-alphanumerics with `-`).
+Write to `{OUTPUT_DIR}/{slug}-{source_hash}.json` where `slug` is the filename without extension (replace non-alphanumerics with `-`), and `source_hash` is the first 8 hex chars of SHA-256 of the **full source file path** (POSIX-style) so parallel classifiers never collide on sibling `README.md` files.
 
 JSON schema:
 

agents/gsd-executor.md

@@ -72,10 +72,11 @@ if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 
 Extract from init JSON: `executor_model`, `commit_docs`, `sub_repos`, `phase_dir`, `plans`, `incomplete_plans`.
 
-Also read STATE.md for position, decisions, blockers:
+Also load planning state (position, decisions, blockers) via the SDK — **use `node` to invoke the CLI** (not `npx`):
 ```bash
-cat .planning/STATE.md 2>/dev/null
+node ./node_modules/@gsd-build/sdk/dist/cli.js query state.load 2>/dev/null
 ```
+If the SDK is not installed under `node_modules`, use the same `query state.load` argv with your local `gsd-sdk` CLI on `PATH`.
 
 If STATE.md missing but .planning/ exists: offer to reconstruct or continue without.
 If .planning/ missing: Error — project not initialized.

agents/gsd-plan-checker.md

@@ -639,11 +639,11 @@ Extract from init JSON: `phase_dir`, `phase_number`, `has_plans`, `plan_count`.
 Orchestrator provides CONTEXT.md content in the verification prompt. If provided, parse for locked decisions, discretion areas, deferred ideas.
 
 ```bash
-ls "$phase_dir"/*-PLAN.md 2>/dev/null
-# Read research for Nyquist validation data
-cat "$phase_dir"/*-RESEARCH.md 2>/dev/null
-gsd-sdk query roadmap.get-phase "$phase_number"
-ls "$phase_dir"/*-BRIEF.md 2>/dev/null
+node ./node_modules/@gsd-build/sdk/dist/cli.js query phase.list-plans "$phase_number"
+# Research / brief artifacts (deterministic listing)
+node ./node_modules/@gsd-build/sdk/dist/cli.js query phase.list-artifacts "$phase_number" --type research
+node ./node_modules/@gsd-build/sdk/dist/cli.js query roadmap.get-phase "$phase_number"
+node ./node_modules/@gsd-build/sdk/dist/cli.js query phase.list-artifacts "$phase_number" --type summary
 ```
 
 **Extract:** Phase goal, requirements (decompose goal), locked decisions, deferred ideas.
@@ -729,10 +729,11 @@ The `tasks` array in the result shows each task's completeness:
 
 **Check:** valid task type (auto, checkpoint:*, tdd), auto tasks have files/action/verify/done, action is specific, verify is runnable, done is measurable.
 
-**For manual validation of specificity** (`verify.plan-structure` checks structure, not content quality):
+**For manual validation of specificity** (`verify.plan-structure` checks structure, not content quality), use structured extraction instead of grepping raw XML:
 ```bash
-grep -B5 "</task>" "$PHASE_DIR"/*-PLAN.md | grep -v "<verify>"
+node ./node_modules/@gsd-build/sdk/dist/cli.js query plan.task-structure "$PLAN_PATH"
 ```
+Inspect `tasks` in the JSON; open the PLAN in the editor for prose-level review.
 
 ## Step 6: Verify Dependency Graph
 
@@ -757,8 +758,8 @@ Missing: No mention of fetch/API call → Issue: Key link not planned
 ## Step 8: Assess Scope
 
 ```bash
-grep -c "<task" "$PHASE_DIR"/$PHASE-01-PLAN.md
-grep "files_modified:" "$PHASE_DIR"/$PHASE-01-PLAN.md
+node ./node_modules/@gsd-build/sdk/dist/cli.js query plan.task-structure "$PHASE_DIR/$PHASE-01-PLAN.md"
+node ./node_modules/@gsd-build/sdk/dist/cli.js query frontmatter.get "$PHASE_DIR/$PHASE-01-PLAN.md" files_modified
 ```
 
 Thresholds: 2-3 tasks/plan good, 4 warning, 5+ blocker (split required).

agents/gsd-planner.md

@@ -812,10 +812,11 @@ if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 
 Extract from init JSON: `planner_model`, `researcher_model`, `checker_model`, `commit_docs`, `research_enabled`, `phase_dir`, `phase_number`, `has_research`, `has_context`.
 
-Also read STATE.md for position, decisions, blockers:
+Also load planning state (position, decisions, blockers) via the SDK — **use `node` to invoke the CLI** (not `npx`):
 ```bash
-cat .planning/STATE.md 2>/dev/null
+node ./node_modules/@gsd-build/sdk/dist/cli.js query state.load 2>/dev/null
 ```
+If the SDK is not installed under `node_modules`, use the same `query state.load` argv with your local `gsd-sdk` CLI on `PATH`.
 
 If STATE.md missing but .planning/ exists, offer to reconstruct or continue without.
 </step>

agents/gsd-roadmapper.md

@@ -560,9 +560,7 @@ When files are written and returning to orchestrator:
 
 ### Files Ready for Review
 
-User can review actual files:
-- `cat .planning/ROADMAP.md`
-- `cat .planning/STATE.md`
+User can review actual files in the editor or via SDK queries (e.g. `node ./node_modules/@gsd-build/sdk/dist/cli.js query roadmap.analyze` and `query state.load`) instead of ad-hoc shell `cat`.
 
 {If gaps found during creation:}