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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get-shit-done/workflows/code-review.md

@@ -17,7 +17,7 @@ Parse arguments and load project state:
 
 ```bash
 PHASE_ARG="${1}"
-INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init phase-op "${PHASE_ARG}")
+INIT=$(gsd-sdk query init.phase-op "${PHASE_ARG}")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
@@ -74,7 +74,7 @@ fi
 Check if code review is enabled via config:
 
 ```bash
-CODE_REVIEW_ENABLED=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.code_review 2>/dev/null || echo "true")
+CODE_REVIEW_ENABLED=$(gsd-sdk query config-get workflow.code_review 2>/dev/null || echo "true")
 ```
 
 If CODE_REVIEW_ENABLED is "false":
@@ -90,14 +90,14 @@ Default is true — only skip on explicit false. This check runs AFTER phase val
 Determine review depth with priority order:
 
 1. DEPTH_OVERRIDE from --depth flag (highest priority)
-2. Config value: `node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.code_review_depth 2>/dev/null`
+2. Config value: `gsd-sdk query config-get workflow.code_review_depth 2>/dev/null`
 3. Default: "standard"
 
 ```bash
 if [ -n "$DEPTH_OVERRIDE" ]; then
   REVIEW_DEPTH="$DEPTH_OVERRIDE"
 else
-  CONFIG_DEPTH=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.code_review_depth 2>/dev/null || echo "")
+  CONFIG_DEPTH=$(gsd-sdk query config-get workflow.code_review_depth 2>/dev/null || echo "")
   REVIEW_DEPTH="${CONFIG_DEPTH:-standard}"
 fi
 ```
@@ -395,7 +395,7 @@ if [ -f "${REVIEW_PATH}" ]; then
     echo "REVIEW.md created at ${REVIEW_PATH}"
     
     if [ "$COMMIT_DOCS" = "true" ]; then
-      node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit \
+      gsd-sdk query commit \
         "docs(${PADDED_PHASE}): add code review report" \
         --files "${REVIEW_PATH}"
     fi