feat: Phase 2 caller migration — gsd-sdk query in workflows, agents, commands (#2179)

* feat: Phase 2 caller migration — gsd-sdk query in workflows (#2122)

Cherry-picked orchestration rewrites from feat/sdk-foundation (#2008, 4018fee) onto current main, resolving conflicts to keep upstream worktree guards and post-merge test gate. SDK stub registry omitted (out of Phase 2 scope per #2122).

Refs: #2122 #2008
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* docs: add gsd-sdk query migration blurb

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* docs(workflows): extend Phase 2 gsd-sdk query caller migration

- Swap node gsd-tools.cjs for gsd-sdk query in review, plan-phase, execute-plan,
  ship, extract_learnings, ai-integration-phase, eval-review, next, thread
- Document graphify CJS-only in gsd-planner; dual-path in CLI-TOOLS and ARCHITECTURE
- Update tests: workstreams gsd-sdk path, thread frontmatter.get, workspace init.*,
  CRLF-safe autonomous frontmatter parse
- CHANGELOG: Phase 2 caller migration scope

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* docs(phase2): USER-GUIDE + remaining gsd-sdk query call sites

- USER-GUIDE: dual-path CLI section; state validate/sync use full CJS path
- Commands: debug (config-get+tdd), quick (security note), intel Task prompt
- Agent: gsd-debug-session-manager resolve-model via jq
- Workflows: milestone-summary, forensics, next, complete-milestone/verify-work
  (audit-open CJS notes), discuss-phase, progress, verify-phase, add/insert/remove
  phase, transition, manager, quick workflow; remove-phase commit without --files
- Test: quick-session-management accepts frontmatter.get
- CHANGELOG: Phase 2 follow-up bullet

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* docs(phase2): align gsd-sdk query examples in commands and agents

- init.* query names; frontmatter.get uses positional field name
- state.* handlers use positional args; commit uses positional paths
- CJS-only notes for from-gsd2 and graphify; learnings.query wording
- CHANGELOG: Phase 2 orchestration doc pass

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* docs(phase2): normalize gsd-sdk query commit to positional file paths

- Strip --files from commit examples in workflows, references, commands
- Keep commit-to-subrepo ... --files (separate handler)
- git-planning-commit.md: document positional args
- Tests: new-project commit line, state.record-session, gates CRLF, roadmap.analyze
- CHANGELOG [Unreleased]

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* feat(sdk): gsd-sdk query parity with gsd-tools and PR 2179 registry fixes

- Route query via longest-prefix match and dotted single-token expansion; fall back
  to runGsdToolsQuery (same argv as node gsd-tools.cjs) for full CLI coverage.
- Parse gsd-sdk query permissively so gsd-tools flags (--json, --verify, etc.) are
  not rejected by strict parseArgs.
- resolveGsdToolsPath: honor GSD_TOOLS_PATH; prefer bundled get-shit-done copy
  over project .claude installs; export runGsdToolsQuery from the SDK.
- Fix gsd-tools audit-open (core.output; pass object for --json JSON).
- Register summary-extract as alias of summary.extract; fix audit-fix workflow to
  call audit-uat instead of invalid init.audit-uat (PR review).

Updates QUERY-HANDLERS.md and CHANGELOG [Unreleased].

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* fix(sdk): Phase 2 scope — Trek-e review (#2179, #2122)

- Remove gsd-sdk query passthrough to gsd-tools.cjs; drop GSD_TOOLS_PATH
- Consolidate argv routing in resolveQueryArgv(); update USAGE and QUERY-HANDLERS
- Surface @file: read failures in GSDTools.parseOutput
- execute-plan: defer Task Commit Protocol to gsd-executor
- stale-colon-refs: skip .planning/ and root CLAUDE.md (gitignored overlays)
- CHANGELOG [Unreleased]: maintainer review and routing notes

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agents/gsd-code-fixer.md

@@ -194,7 +194,7 @@ The **Fix:** section may contain:
 If a finding references multiple files (in Fix section or Issue section):
 - Collect ALL file paths into `files` array
 - Apply fix to each file
-- Commit all modified files atomically (single commit, multiple files in `--files` list)
+- Commit all modified files atomically (single commit, list every file path after the message — `commit` uses positional paths, not `--files`)
 
 **Parsing Rules:**
 
@@ -308,20 +308,21 @@ For each finding in sorted order:
 
 **If verification passed:**
 
-Use gsd-tools commit command with conventional format:
+Use `gsd-sdk query commit` with conventional format (message first, then every staged file path):
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit \
+gsd-sdk query commit \
   "fix({padded_phase}): {finding_id} {short_description}" \
-  --files {all_modified_files}
+  {all_modified_files}
 ```
 
 Examples:
 - `fix(02): CR-01 fix SQL injection in auth.py`
 - `fix(03): WR-05 add null check before array access`
 
-**Multiple files:** List ALL modified files in `--files` (space-separated):
+**Multiple files:** List ALL modified files after the message (space-separated):
 ```bash
---files src/api/auth.ts src/types/user.ts tests/auth.test.ts
+gsd-sdk query commit "fix(02): CR-01 ..." \
+  src/api/auth.ts src/types/user.ts tests/auth.test.ts
 ```
 
 **Extract commit hash:**
@@ -442,7 +443,7 @@ _Iteration: {N}_
 
 **DO record which files will be touched** before every fix attempt — this is your rollback list. Rollback is `git checkout -- {file}`, not content capture.
 
-**DO commit each fix atomically** — one commit per finding, listing ALL modified files in `--files` argument.
+**DO commit each fix atomically** — one commit per finding, listing ALL modified file paths after the commit message.
 
 **DO use Edit tool (preferred)** over Write tool for targeted changes. Edit provides better diff visibility.
 
@@ -504,7 +505,7 @@ Fixes are committed **per-finding**. This has operational implications:
 
 - [ ] All in-scope findings attempted (either fixed or skipped with reason)
 - [ ] Each fix committed atomically with `fix({padded_phase}): {id} {description}` format
-- [ ] All modified files listed in each commit's `--files` argument (multi-file fix support)
+- [ ] All modified files listed after each commit message (multi-file fix support)
 - [ ] REVIEW-FIX.md created with accurate counts, status, and iteration number
 - [ ] No source files left in broken state (failed fixes rolled back via git checkout)
 - [ ] No partial or uncommitted changes remain after execution