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/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