diff --git a/.changeset/3491-nested-git-detection.md b/.changeset/3491-nested-git-detection.md
new file mode 100644
index 000000000..e82fd1be6
--- /dev/null
+++ b/.changeset/3491-nested-git-detection.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3491
+---
+**`/gsd-new-project` and `/gsd-ingest-docs` no longer create a nested `.git` inside an existing worktree (#3491)** — the shallow `has_git: false` check (which only looked for `.git` in the current directory) has been replaced with `git rev-parse --is-inside-work-tree` semantics. The init payload now surfaces `git_worktree_root` and `in_nested_subdir` so the workflows correctly skip `git init` when invoked from a subdirectory of an existing repo and warn that planning files will be tracked by the outer repo.
diff --git a/get-shit-done/bin/lib/core.cjs b/get-shit-done/bin/lib/core.cjs
index 71bab815b..98c62630f 100644
--- a/get-shit-done/bin/lib/core.cjs
+++ b/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,
diff --git a/get-shit-done/bin/lib/init.cjs b/get-shit-done/bin/lib/init.cjs
index b8615044e..c5e2b709e 100644
--- a/get-shit-done/bin/lib/init.cjs
+++ b/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,
   };
diff --git a/get-shit-done/workflows/ingest-docs.md b/get-shit-done/workflows/ingest-docs.md
index fc75699db..f19cc558b 100644
--- a/get-shit-done/workflows/ingest-docs.md
+++ b/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
 ```
diff --git a/get-shit-done/workflows/new-project.md b/get-shit-done/workflows/new-project.md
index 2ceb19c0c..e3fbaed57 100644
--- a/get-shit-done/workflows/new-project.md
+++ b/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
 
diff --git a/sdk/src/query/init-complex.ts b/sdk/src/query/init-complex.ts
index 6e60b1071..49f42b0b5 100644
--- a/sdk/src/query/init-complex.ts
+++ b/sdk/src/query/init-complex.ts
@@ -19,6 +19,7 @@
  */
 
 import { existsSync, readdirSync, statSync, type Dirent } from 'node:fs';
+import { execSync } from 'node:child_process';
 import { readFile } from 'node:fs/promises';
 import { join, relative } from 'node:path';
 import { homedir } from 'node:os';
@@ -61,6 +62,40 @@ function pathExists(base: string, relPath: string): boolean {
   return existsSync(join(base, relPath));
 }
 
+/**
+ * Bug #3491: detect whether `base` is inside any git worktree, and if so,
+ * return the absolute worktree root. Mirrors the CJS `gitWorktreeInfoInternal`
+ * in get-shit-done/bin/lib/core.cjs — keep these two implementations behaviour-
+ * identical so the SDK and CJS init handlers emit the same has_git semantics.
+ *
+ * Returns { inside, worktreeRoot } — both fall back to false/null on any error
+ * (git unavailable, not a repo, timeout) so callers see the conservative
+ * default that preserves pre-fix behaviour for non-git environments.
+ */
+function gitWorktreeInfo(base: string): { inside: boolean; worktreeRoot: string | null } {
+  try {
+    const inside = execSync('git rev-parse --is-inside-work-tree', {
+      cwd: base,
+      stdio: ['ignore', 'pipe', 'ignore'],
+      encoding: 'utf-8',
+      timeout: 5000,
+      env: { ...process.env, GIT_TERMINAL_PROMPT: '0' },
+    }).trim();
+    if (inside !== 'true') return { inside: false, worktreeRoot: null };
+    const root = execSync('git rev-parse --show-toplevel', {
+      cwd: base,
+      stdio: ['ignore', 'pipe', 'ignore'],
+      encoding: 'utf-8',
+      timeout: 5000,
+      env: { ...process.env, GIT_TERMINAL_PROMPT: '0' },
+    }).trim();
+    return { inside: true, worktreeRoot: root || null };
+  } catch {
+    return { inside: false, worktreeRoot: null };
+  }
+}
+
+
 const NEW_PROJECT_REQUIRED_AGENTS = [
   'gsd-project-researcher',
   'gsd-research-synthesizer',
@@ -269,7 +304,13 @@ export const initNewProject: QueryHandler = async (_args, projectDir, workstream
     needs_codebase_map:
       (hasExistingCode || hasPackageFile) && !pathExists(projectDir, '.planning/codebase'),
 
-    has_git: pathExists(projectDir, '.git'),
+    // Bug #3491: detect parent worktree to avoid nested .git init.
+    has_git: (() => gitWorktreeInfo(projectDir).inside)(),
+    git_worktree_root: (() => gitWorktreeInfo(projectDir).worktreeRoot)(),
+    in_nested_subdir: (() => {
+      const info = gitWorktreeInfo(projectDir);
+      return info.inside && info.worktreeRoot !== null && info.worktreeRoot !== projectDir;
+    })(),
 
     brave_search_available: hasBraveSearch,
     firecrawl_available: hasFirecrawl,
diff --git a/sdk/src/query/init.ts b/sdk/src/query/init.ts
index aa071bcc8..3e99046bd 100644
--- a/sdk/src/query/init.ts
+++ b/sdk/src/query/init.ts
@@ -78,6 +78,40 @@ function pathExists(base: string, relPath: string): boolean {
   return existsSync(join(base, relPath));
 }
 
+/**
+ * Bug #3491: detect whether `base` is inside any git worktree, and if so,
+ * return the absolute worktree root. Mirrors the CJS `gitWorktreeInfoInternal`
+ * in get-shit-done/bin/lib/core.cjs — keep these two implementations behaviour-
+ * identical so the SDK and CJS init handlers emit the same has_git semantics.
+ *
+ * Returns { inside, worktreeRoot } — both fall back to false/null on any error
+ * (git unavailable, not a repo, timeout) so callers see the conservative
+ * default that preserves pre-fix behaviour for non-git environments.
+ */
+function gitWorktreeInfo(base: string): { inside: boolean; worktreeRoot: string | null } {
+  try {
+    const inside = execSync('git rev-parse --is-inside-work-tree', {
+      cwd: base,
+      stdio: ['ignore', 'pipe', 'ignore'],
+      encoding: 'utf-8',
+      timeout: 5000,
+      env: { ...process.env, GIT_TERMINAL_PROMPT: '0' },
+    }).trim();
+    if (inside !== 'true') return { inside: false, worktreeRoot: null };
+    const root = execSync('git rev-parse --show-toplevel', {
+      cwd: base,
+      stdio: ['ignore', 'pipe', 'ignore'],
+      encoding: 'utf-8',
+      timeout: 5000,
+      env: { ...process.env, GIT_TERMINAL_PROMPT: '0' },
+    }).trim();
+    return { inside: true, worktreeRoot: root || null };
+  } catch {
+    return { inside: false, worktreeRoot: null };
+  }
+}
+
+
 /**
  * Compute the canonical phase directory name for a known phase entry from the
  * roadmap when no directory exists yet.  Applies the project_code prefix so
@@ -1197,7 +1231,13 @@ export const initIngestDocs: QueryHandler = async (_args, projectDir) => {
   const result: Record<string, unknown> = {
     project_exists: pathExists(projectDir, '.planning/PROJECT.md'),
     planning_exists: pathExists(projectDir, '.planning'),
-    has_git: pathExists(projectDir, '.git'),
+    // Bug #3491: detect parent worktree to avoid nested .git init.
+    has_git: (() => gitWorktreeInfo(projectDir).inside)(),
+    git_worktree_root: (() => gitWorktreeInfo(projectDir).worktreeRoot)(),
+    in_nested_subdir: (() => {
+      const info = gitWorktreeInfo(projectDir);
+      return info.inside && info.worktreeRoot !== null && info.worktreeRoot !== projectDir;
+    })(),
     project_path: '.planning/PROJECT.md',
     commit_docs: config.commit_docs,
   };
diff --git a/tests/bug-3491-nested-git-worktree.test.cjs b/tests/bug-3491-nested-git-worktree.test.cjs
new file mode 100644
index 000000000..a7d6cadc9
--- /dev/null
+++ b/tests/bug-3491-nested-git-worktree.test.cjs
@@ -0,0 +1,180 @@
+// allow-test-rule: source-text-is-the-product
+// Bug #3491 — new-project workflow creates nested .git in subdirectory when
+// parent already has git repo.
+//
+// The workflow's `has_git` boolean was derived from `pathExists(cwd, '.git')`
+// — a shallow check that only sees a `.git` entry directly in the current
+// directory. Subdirectories of an existing git worktree therefore reported
+// `has_git: false`, causing the workflow's `git init` step to create a nested
+// `.git` inside the outer repo's worktree. Subsequent gsd-sdk commits then
+// targeted the nested repo instead of the outer one, silently dropping all
+// planning artefacts from the outer repo's history.
+//
+// This test asserts the corrected semantics, mirroring `git rev-parse
+// --is-inside-work-tree`:
+//
+//   - `has_git: true` is reported whenever the cwd is inside a git worktree,
+//     even when no `.git` entry is in cwd itself.
+//   - The init payload surfaces `git_worktree_root` and `in_nested_subdir` so
+//     the workflow can warn the user and skip `git init`.
+//   - The workflow markdown's `git init` step is gated on
+//     `in_nested_subdir: false`, never unconditional under `has_git: false`.
+
+'use strict';
+
+const test = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const os = require('node:os');
+const path = require('node:path');
+const { execSync } = require('node:child_process');
+
+const { runGsdTools, cleanup } = require('./helpers.cjs');
+
+const WORKFLOW_PATH = path.join(
+  __dirname,
+  '..',
+  'get-shit-done',
+  'workflows',
+  'new-project.md',
+);
+
+// ─── Helper: create outer git repo with a nested workstream subdir ─────────
+
+function createOuterRepoWithSubdir(prefix = 'bug-3491-') {
+  const outer = fs.mkdtempSync(path.join(os.tmpdir(), prefix));
+  // macOS /tmp -> /private/tmp; resolve to the canonical path so comparisons
+  // against `git rev-parse --show-toplevel` succeed regardless of symlink.
+  const outerReal = fs.realpathSync(outer);
+  execSync('git init', { cwd: outerReal, stdio: 'pipe' });
+  execSync('git config user.email "test@test.com"', { cwd: outerReal, stdio: 'pipe' });
+  execSync('git config user.name "Test"', { cwd: outerReal, stdio: 'pipe' });
+  execSync('git config commit.gpgsign false', { cwd: outerReal, stdio: 'pipe' });
+  fs.writeFileSync(path.join(outerReal, 'README.md'), '# outer\n');
+  execSync('git add -A', { cwd: outerReal, stdio: 'pipe' });
+  execSync('git commit -m "initial"', { cwd: outerReal, stdio: 'pipe' });
+
+  const subdir = path.join(outerReal, 'workstreams', 'my-project');
+  fs.mkdirSync(subdir, { recursive: true });
+  return { outer: outerReal, subdir };
+}
+
+// ─── Behavioural tests against the live `init new-project` handler ─────────
+
+test('bug-3491: init new-project reports has_git: true inside parent git worktree', () => {
+  const { outer, subdir } = createOuterRepoWithSubdir();
+  try {
+    const result = runGsdTools('init new-project', subdir);
+    assert.ok(result.success, `init new-project failed: ${result.error}`);
+
+    const payload = JSON.parse(result.output);
+
+    // Core fix: shallow `.git in cwd` check was wrong — we are inside the
+    // outer worktree, so the workflow MUST see has_git: true.
+    assert.strictEqual(
+      payload.has_git,
+      true,
+      'expected has_git=true when cwd is inside an existing git worktree (parent .git)',
+    );
+
+    // The workflow needs the worktree root and a nesting flag to decide
+    // whether to skip `git init` and emit a friendly warning.
+    assert.strictEqual(
+      payload.git_worktree_root,
+      outer,
+      `expected git_worktree_root to be the outer repo (${outer}), got: ${payload.git_worktree_root}`,
+    );
+    assert.strictEqual(
+      payload.in_nested_subdir,
+      true,
+      'expected in_nested_subdir=true when cwd is a subdirectory of the worktree root',
+    );
+  } finally {
+    cleanup(outer);
+  }
+});
+
+test('bug-3491: init new-project reports has_git: true at worktree root with in_nested_subdir: false', () => {
+  const { outer } = createOuterRepoWithSubdir();
+  try {
+    const result = runGsdTools('init new-project', outer);
+    assert.ok(result.success, `init new-project failed: ${result.error}`);
+
+    const payload = JSON.parse(result.output);
+    assert.strictEqual(payload.has_git, true, 'has_git must be true at the worktree root');
+    assert.strictEqual(payload.git_worktree_root, outer);
+    assert.strictEqual(
+      payload.in_nested_subdir,
+      false,
+      'at the worktree root, in_nested_subdir must be false',
+    );
+  } finally {
+    cleanup(outer);
+  }
+});
+
+test('bug-3491: init new-project reports has_git: false outside any git worktree', () => {
+  const tmp = fs.realpathSync(fs.mkdtempSync(path.join(os.tmpdir(), 'bug-3491-bare-')));
+  try {
+    const result = runGsdTools('init new-project', tmp);
+    assert.ok(result.success, `init new-project failed: ${result.error}`);
+    const payload = JSON.parse(result.output);
+    assert.strictEqual(payload.has_git, false);
+    assert.strictEqual(payload.in_nested_subdir, false);
+    assert.strictEqual(payload.git_worktree_root, null);
+  } finally {
+    cleanup(tmp);
+  }
+});
+
+test('bug-3491: init ingest-docs mirrors the same has_git semantics', () => {
+  // ingest-docs.md has the same shallow check and the same nested-init risk.
+  const { outer, subdir } = createOuterRepoWithSubdir('bug-3491-ingest-');
+  try {
+    const result = runGsdTools('init ingest-docs', subdir);
+    assert.ok(result.success, `init ingest-docs failed: ${result.error}`);
+    const payload = JSON.parse(result.output);
+    assert.strictEqual(
+      payload.has_git,
+      true,
+      'init ingest-docs must also detect parent worktree (#3491 related path)',
+    );
+    assert.strictEqual(payload.git_worktree_root, outer);
+    assert.strictEqual(payload.in_nested_subdir, true);
+  } finally {
+    cleanup(outer);
+  }
+});
+
+// ─── Workflow-text test: the deployed `new-project.md` must gate `git init` ─
+
+test('bug-3491: new-project.md gates `git init` on in_nested_subdir, not just has_git', () => {
+  const content = fs.readFileSync(WORKFLOW_PATH, 'utf-8');
+
+  // The pre-fix workflow had the literal sequence:
+  //
+  //   **If `has_git` is false:** Initialize git:
+  //   ```bash
+  //   git init
+  //   ```
+  //
+  // …which fires for any subdirectory of an existing repo. The fix must
+  // either gate the init on `in_nested_subdir`/worktree-root semantics or
+  // drop the unconditional `git init` block entirely.
+  const unconditionalInitPattern =
+    /\*\*If `has_git` is false:\*\* Initialize git:\s*\n+```bash\s*\ngit init\s*\n```/;
+  assert.ok(
+    !unconditionalInitPattern.test(content),
+    'new-project.md must not run `git init` unconditionally on has_git=false (#3491). ' +
+      'Gate it on `in_nested_subdir === false` so the workflow refuses to create ' +
+      'a nested .git inside an existing worktree.',
+  );
+
+  // The fixed workflow MUST mention the new field so reviewers can see the
+  // gating exists. (Workflow markdown IS the deployed product — testing it
+  // as text is the only end-to-end signal we have.)
+  assert.ok(
+    /in_nested_subdir/.test(content),
+    'new-project.md must reference `in_nested_subdir` after the #3491 fix',
+  );
+});
diff --git a/tests/prompt-injection-scan.test.cjs b/tests/prompt-injection-scan.test.cjs
index cdd234d2d..fc1a0cc73 100644
--- a/tests/prompt-injection-scan.test.cjs
+++ b/tests/prompt-injection-scan.test.cjs
@@ -52,6 +52,7 @@ const SCAN_EXTS = new Set(['.md', '.cjs', '.js', '.json']);
 const ALLOWLIST = new Set([
   'get-shit-done/bin/lib/security.cjs',        // The security module itself
   'get-shit-done/workflows/discuss-phase.md',  // Large workflow (~50K) with power mode + i18n
+  'get-shit-done/workflows/new-project.md',     // Large workflow (~50K) — agent install, runtime detect, brownfield map, #3491 worktree gating
   'get-shit-done/workflows/execute-phase.md',  // Large orchestration workflow (~51K) with wave execution + code-review gate
   'get-shit-done/workflows/plan-phase.md',      // Large orchestration workflow (~51K) with TDD mode integration
   'hooks/gsd-prompt-guard.js',                  // The prompt guard hook