docs(sdk): registry docs and gsd-sdk query call sites (#2302 Track B) (#2340)

* 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

* docs(sdk): registry docs and gsd-sdk query call sites (#2302 Track B)

Update CHANGELOG, architecture and user guides, workflow call sites, and read-guard tests for gsd-sdk query; sync ARCHITECTURE.md command/workflow counts and directory-tree totals with the repo (80 commands, 77 workflows).

Address CodeRabbit: fix markdown tables and emphasis; align CLI-TOOLS GSDTools and state.read docs with implementation; correct roadmap handler name in universal-anti-patterns; resolve settings workflow config path without relying on config_path from state.load.

Refs gsd-build/get-shit-done#2340

* test: raise planner character extraction limit to 48K

* fix(sdk): resolve build TS error and doc conflict markers

docs/zh-CN/references/decimal-phase-calculation.md

@@ -2,11 +2,11 @@
 
 为紧急插入计算下一个小数阶段编号。
 
-## 使用 gsd-tools
+## 使用 gsd-sdk query
 
 ```bash
 # 获取阶段 6 之后的下一个小数阶段
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phase next-decimal 6
+gsd-sdk query phase.next-decimal 6
 ```
 
 输出：
@@ -32,14 +32,13 @@ node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phase next-decimal 6
 ## 提取值
 
 ```bash
-DECIMAL_INFO=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phase next-decimal "${AFTER_PHASE}")
-DECIMAL_PHASE=$(printf '%s\n' "$DECIMAL_INFO" | jq -r '.next')
-BASE_PHASE=$(printf '%s\n' "$DECIMAL_INFO" | jq -r '.base_phase')
+DECIMAL_PHASE=$(gsd-sdk query phase.next-decimal "${AFTER_PHASE}" --pick next)
+BASE_PHASE=$(gsd-sdk query phase.next-decimal "${AFTER_PHASE}" --pick base_phase)
 ```
 
 或使用 --raw 标志：
 ```bash
-DECIMAL_PHASE=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phase next-decimal "${AFTER_PHASE}" --raw)
+DECIMAL_PHASE=$(gsd-sdk query phase.next-decimal "${AFTER_PHASE}" --raw)
 # 返回: 06.1
 ```
 
@@ -57,9 +56,9 @@ DECIMAL_PHASE=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phase next-
 小数阶段目录使用完整的小数编号：
 
 ```bash
-SLUG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" generate-slug "$DESCRIPTION" --raw)
+SLUG=$(gsd-sdk query generate-slug "$DESCRIPTION" --raw)
 PHASE_DIR=".planning/phases/${DECIMAL_PHASE}-${SLUG}"
 mkdir -p "$PHASE_DIR"
 ```
 
-示例：`.planning/phases/06.1-fix-critical-auth-bug/`
+示例：`.planning/phases/06.1-fix-critical-auth-bug/`

docs/zh-CN/references/git-integration.md

@@ -51,7 +51,7 @@ Phases:
 提交内容：
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs: initialize [project-name] ([N] phases)" --files .planning/
+gsd-sdk query commit "docs: initialize [project-name] ([N] phases)" .planning/
 ```
 
 </format>
@@ -129,7 +129,7 @@ SUMMARY: .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md
 提交内容：
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-PLAN.md .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" .planning/phases/XX-name/{phase}-{plan}-PLAN.md .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md
 ```
 
 **注意：** 代码文件不包含 - 已按任务提交。
@@ -149,7 +149,7 @@ Current: [task name]
 提交内容：
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "wip: [phase-name] paused at task [X]/[Y]" --files .planning/
+gsd-sdk query commit "wip: [phase-name] paused at task [X]/[Y]" .planning/
 ```
 
 </format>

docs/zh-CN/references/git-planning-commit.md

@@ -1,13 +1,15 @@
 # Git 规划提交
 
-使用 gsd-tools CLI 提交规划工件，它会自动检查 `commit_docs` 配置和 gitignore 状态。
+通过 `gsd-sdk query commit` 提交规划工件，它会自动检查 `commit_docs` 配置和 gitignore 状态（与旧版 `gsd-tools.cjs commit` 行为相同）。
 
 ## 通过 CLI 提交
 
-始终使用 `gsd-tools.cjs commit` 处理 `.planning/` 文件 — 它会自动处理 `commit_docs` 和 gitignore 检查：
+先传提交说明，再传文件路径（位置参数）。`commit` 不要使用 `--files`（该标志仅用于 `commit-to-subrepo`）。
+
+对 `.planning/` 文件始终使用此方式 —— 它会自动处理 `commit_docs` 与 gitignore 检查：
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs({scope}): {description}" --files .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({scope}): {description}" .planning/STATE.md .planning/ROADMAP.md
 ```
 
 如果 `commit_docs` 为 `false` 或 `.planning/` 被 gitignore，CLI 会返回 `skipped`（带原因）。无需手动条件检查。
@@ -17,7 +19,7 @@ node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs({scope}): {des
 将 `.planning/` 文件变更合并到上次提交：
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "" --files .planning/codebase/*.md --amend
+gsd-sdk query commit "" .planning/codebase/*.md --amend
 ```
 
 ## 提交消息模式
@@ -35,4 +37,4 @@ node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "" --files .planning
 
 - config 中 `commit_docs: false`
 - `.planning/` 被 gitignore
-- 无变更可提交（用 `git status --porcelain .planning/` 检查）
+- 无变更可提交（用 `git status --porcelain .planning/` 检查）

docs/zh-CN/references/planning-config.md

@@ -36,19 +36,19 @@
 - 用户必须将 `.planning/` 添加到 `.gitignore`
 - 适用于：OSS 贡献、客户项目、保持规划私有
 
-**使用 gsd-tools.cjs（推荐）：**
+**使用 `gsd-sdk query`（推荐）：**
 
 ```bash
 # 提交时自动检查 commit_docs + gitignore：
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs: update state" --files .planning/STATE.md
+gsd-sdk query commit "docs: update state" .planning/STATE.md
 
 # 通过 state load 加载配置（返回 JSON）：
-INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state load)
+INIT=$(gsd-sdk query state.load)
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 # commit_docs 在 JSON 输出中可用
 
 # 或使用包含 commit_docs 的 init 命令：
-INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init execute-phase "1")
+INIT=$(gsd-sdk query init.execute-phase "1")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 # commit_docs 包含在所有 init 命令输出中
 ```
@@ -58,7 +58,7 @@ if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 **通过 CLI 提交（自动处理检查）：**
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs: update state" --files .planning/STATE.md
+gsd-sdk query commit "docs: update state" .planning/STATE.md
 ```
 
 CLI 在内部检查 `commit_docs` 配置和 gitignore 状态 —— 无需手动条件判断。
@@ -146,14 +146,14 @@ CLI 在内部检查 `commit_docs` 配置和 gitignore 状态 —— 无需手动
 
 使用 `init execute-phase` 返回所有配置为 JSON：
 ```bash
-INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init execute-phase "1")
+INIT=$(gsd-sdk query init.execute-phase "1")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 # JSON 输出包含：branching_strategy, phase_branch_template, milestone_branch_template
 ```
 
 或使用 `state load` 获取配置值：
 ```bash
-INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state load)
+INIT=$(gsd-sdk query state.load)
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 # 从 JSON 解析 branching_strategy, phase_branch_template, milestone_branch_template
 ```