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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docs/ARCHITECTURE.md

@@ -54,7 +54,7 @@ GSD is a **meta-prompting framework** that sits between the user and AI coding a
        │              │                 │
 ┌──────▼──────────────▼─────────────────▼──────────────┐
 │              CLI TOOLS LAYER                          │
-│   get-shit-done/bin/gsd-tools.cjs                     │
+│   gsd-sdk query (sdk/src/query) + gsd-tools.cjs       │
 │   (State, config, phase, roadmap, verify, templates)  │
 └──────────────────────┬───────────────────────────────┘
                        │
@@ -76,7 +76,7 @@ Every agent spawned by an orchestrator gets a clean context window (up to 200K t
 ### 2. Thin Orchestrators
 
 Workflow files (`get-shit-done/workflows/*.md`) never do heavy lifting. They:
-- Load context via `gsd-tools.cjs init <workflow>`
+- Load context via `gsd-sdk query init.<workflow>` (or legacy `gsd-tools.cjs init <workflow>`)
 - Spawn specialized agents with focused prompts
 - Collect results and route to the next step
 - Update state between steps
@@ -118,7 +118,7 @@ User-facing entry points. Each file contains YAML frontmatter (name, description
 ### Workflows (`get-shit-done/workflows/*.md`)
 
 Orchestration logic that commands reference. Contains the step-by-step process including:
-- Context loading via `gsd-tools.cjs init`
+- Context loading via `gsd-sdk query` init handlers (or legacy `gsd-tools.cjs init`)
 - Agent spawn instructions with model resolution
 - Gate/checkpoint definitions
 - State update patterns