fix(workflow): detect nested git worktree in new-project bootstrap (#3491)

The `has_git` boolean returned by `init new-project` and `init ingest-docs`
was derived from a shallow `pathExists(cwd, '.git')` check, so a subdirectory
of an existing repo reported `has_git: false`. The workflow then ran
`git init`, creating a nested `.git` inside the outer worktree and silently
diverting subsequent `gsd-sdk commit` calls into the nested repo.

Replace the shallow check with `git rev-parse --is-inside-work-tree`
semantics in both CJS (`get-shit-done/bin/lib/init.cjs`) and TS
(`sdk/src/query/init.ts`, `sdk/src/query/init-complex.ts`) handlers via a new
shared `gitWorktreeInfoInternal` helper, and expose `git_worktree_root` +
`in_nested_subdir` so the workflows can refuse `git init` inside an existing
worktree and warn that planning files will track to the outer repo.

Regression test: `tests/bug-3491-nested-git-worktree.test.cjs`.

Fixes #3491

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

get-shit-done/bin/lib/core.cjs

@@ -1535,6 +1535,48 @@ function pathExistsInternal(cwd, targetPath) {
   }
 }
 
+/**
+ * Detect whether `cwd` sits inside a git worktree, and if so, return the
+ * absolute path of the worktree root.
+ *
+ * Bug #3491: the previous shallow `pathExistsInternal(cwd, '.git')` check
+ * only saw a `.git` entry directly in cwd, so subdirectories of an existing
+ * repo reported `has_git: false` and the new-project workflow then ran
+ * `git init` — creating a nested `.git` inside the outer repo's worktree.
+ *
+ * Mirrors `git rev-parse --is-inside-work-tree` semantics. Uses the existing
+ * `execGit` seam so behaviour is consistent with the rest of the toolchain
+ * (non-interactive env, 10s timeout, mockable in tests).
+ *
+ * Returns: { inside: boolean, worktreeRoot: string | null }
+ *   - inside=true  → cwd is somewhere inside a git worktree
+ *   - inside=false → cwd is not inside any git worktree (or git is unavailable)
+ *
+ * Failure modes (git not installed, command times out, non-zero exit) all
+ * collapse to `{ inside: false, worktreeRoot: null }` — the conservative
+ * default that preserves pre-fix behaviour for environments without git.
+ */
+function gitWorktreeInfoInternal(cwd) {
+  try {
+    const insideResult = execGit(['rev-parse', '--is-inside-work-tree'], { cwd, timeout: 5000 });
+    if (insideResult.exitCode !== 0) {
+      return { inside: false, worktreeRoot: null };
+    }
+    const insideStdout = String(insideResult.stdout || '').trim();
+    if (insideStdout !== 'true') {
+      return { inside: false, worktreeRoot: null };
+    }
+    const rootResult = execGit(['rev-parse', '--show-toplevel'], { cwd, timeout: 5000 });
+    if (rootResult.exitCode !== 0) {
+      return { inside: true, worktreeRoot: null };
+    }
+    const root = String(rootResult.stdout || '').trim();
+    return { inside: true, worktreeRoot: root || null };
+  } catch {
+    return { inside: false, worktreeRoot: null };
+  }
+}
+
 function generateSlugInternal(text) {
   if (!text) return null;
   return text.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '').substring(0, 60);
@@ -1817,6 +1859,7 @@ module.exports = {
   resolveTierEntry,
   _resetRuntimeWarningCacheForTests,
   pathExistsInternal,
+  gitWorktreeInfoInternal,
   generateSlugInternal,
   getMilestoneInfo,
   getMilestonePhaseFilter,

get-shit-done/bin/lib/init.cjs

@@ -5,7 +5,7 @@
 const fs = require('fs');
 const path = require('path');
 const { execGit, platformWriteSync, platformReadSync } = require('./shell-command-projection.cjs');
-const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, generateSlugInternal, getMilestoneInfo, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, normalizePhaseName, toPosixPath, output, error, checkAgentsInstalled, phaseTokenMatches } = require('./core.cjs');
+const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, gitWorktreeInfoInternal, generateSlugInternal, getMilestoneInfo, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, normalizePhaseName, toPosixPath, output, error, checkAgentsInstalled, phaseTokenMatches } = require('./core.cjs');
 const { planningPaths, planningDir, planningRoot } = require('./planning-workspace.cjs');
 const { maskIfSecret } = require('./secrets.cjs');
 const scanPhasePlans = require('./plan-scan.cjs');
@@ -458,8 +458,17 @@ function cmdInitNewProject(cwd, raw) {
     is_brownfield: hasCode || hasPackageFile,
     needs_codebase_map: (hasCode || hasPackageFile) && !pathExistsInternal(cwd, '.planning/codebase'),
 
-    // Git state
-    has_git: pathExistsInternal(cwd, '.git'),
+    // Git state (Bug #3491: detect parent worktree to avoid nested .git init)
+    ...(() => {
+      const info = gitWorktreeInfoInternal(cwd);
+      const worktreeRoot = info.worktreeRoot;
+      const inNestedSubdir = info.inside && worktreeRoot !== null && worktreeRoot !== cwd;
+      return {
+        has_git: info.inside,
+        git_worktree_root: worktreeRoot,
+        in_nested_subdir: inNestedSubdir,
+      };
+    })(),
 
     // Enhanced search
     brave_search_available: hasBraveSearch,
@@ -593,7 +602,17 @@ function cmdInitIngestDocs(cwd, raw) {
   const result = {
     project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
     planning_exists: fs.existsSync(planningRoot(cwd)),
-    has_git: fs.existsSync(path.join(cwd, '.git')),
+    ...(() => {
+      // Bug #3491 — see cmdInitNewProject above. Same shallow-check bug.
+      const info = gitWorktreeInfoInternal(cwd);
+      const worktreeRoot = info.worktreeRoot;
+      const inNestedSubdir = info.inside && worktreeRoot !== null && worktreeRoot !== cwd;
+      return {
+        has_git: info.inside,
+        git_worktree_root: worktreeRoot,
+        in_nested_subdir: inNestedSubdir,
+      };
+    })(),
     project_path: '.planning/PROJECT.md',
     commit_docs: config.commit_docs,
   };

get-shit-done/workflows/ingest-docs.md

@@ -56,7 +56,7 @@ INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init ingest-docs)
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
-Parse `project_exists`, `planning_exists`, `has_git`, `project_path` from INIT.
+Parse `project_exists`, `planning_exists`, `has_git`, `git_worktree_root`, `in_nested_subdir`, `project_path` from INIT.
 
 **Auto-detect MODE** if not set:
 - `planning_exists: true` → `MODE=merge`
@@ -64,7 +64,12 @@ Parse `project_exists`, `planning_exists`, `has_git`, `project_path` from INIT.
 
 If user passed `--mode new` but `.planning/` already exists: display warning and require explicit confirm via `AskUserQuestion` (approve-revise-abort from `references/gate-prompts.md`) before overwriting.
 
-If `has_git: false` and `MODE=new`: initialize git:
+Git initialisation (Bug #3491 — never create a nested `.git` inside an existing worktree):
+
+- If `has_git: true` and `in_nested_subdir: true`: do NOT run `git init`. Surface a warning that planning files will be tracked by the outer repo at `git_worktree_root`.
+- If `has_git: true` and `in_nested_subdir: false`: already at a worktree root, skip `git init`.
+- If `has_git: false` and `MODE=new`: initialize git:
+
 ```bash
 git init
 ```

get-shit-done/workflows/new-project.md

@@ -64,7 +64,7 @@ AGENT_SKILLS_SYNTHESIZER=$(gsd-sdk query agent-skills gsd-research-synthesizer)
 AGENT_SKILLS_ROADMAPPER=$(gsd-sdk query agent-skills gsd-roadmapper)
 ```
 
-Parse JSON for: `researcher_model`, `synthesizer_model`, `roadmapper_model`, `commit_docs`, `project_exists`, `has_codebase_map`, `planning_exists`, `has_existing_code`, `has_package_file`, `is_brownfield`, `needs_codebase_map`, `has_git`, `project_path`, `agents_installed`, `missing_agents`, `agent_runtime`, `agents_dir`, `required_agents`, `required_agents_installed`, `missing_required_agents`, `agent_skill_payloads_available`, `agent_skill_payload_agents`.
+Parse JSON for: `researcher_model`, `synthesizer_model`, `roadmapper_model`, `commit_docs`, `project_exists`, `has_codebase_map`, `planning_exists`, `has_existing_code`, `has_package_file`, `is_brownfield`, `needs_codebase_map`, `has_git`, `git_worktree_root`, `in_nested_subdir`, `project_path`, `agents_installed`, `missing_agents`, `agent_runtime`, `agents_dir`, `required_agents`, `required_agents_installed`, `missing_required_agents`, `agent_skill_payloads_available`, `agent_skill_payload_agents`.
 
 **If `agents_installed` is false:** Display a warning before proceeding:
 ```text
@@ -117,11 +117,11 @@ All subsequent references to the project instruction file use `$INSTRUCTION_FILE
 
 **If `project_exists` is true:** Error — project already initialized. Use `/gsd:progress`.
 
-**If `has_git` is false:** Initialize git:
+**Git init (#3491 — never nest `.git` inside an existing worktree):**
 
-```bash
-git init
-```
+- If `has_git` true and `in_nested_subdir` true: skip `git init`; warn `⚠ Initializing inside existing worktree (${git_worktree_root}); planning files will track to outer repo.`
+- If `has_git` true and `in_nested_subdir` false: skip `git init` (already at worktree root).
+- If `has_git` false: `git init`.
 
 ## 2. Brownfield Offer