From dba91e06d5a4a59c04dfe8c1430b4ab46e8d3209 Mon Sep 17 00:00:00 2001
From: Copilot <copilot@github.com>
Date: Thu, 9 Apr 2026 10:28:17 +0300
Subject: [PATCH 1/4] =?UTF-8?q?fix:=20monorepo=20subfolder=20support=20?=
 =?UTF-8?q?=E2=80=94=20never=20run=20git=20init=20(#939)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

When squad init is run in a subfolder of a monorepo, it previously
ran git init to create a nested repo boundary. This broke monorepo
workflows by creating git-in-git.

Changes:
- Never run git init in init command
- Detect monorepo (cwd != git root) and split file placement:
  - .github/agents/squad.agent.md → git root (Copilot needs it there)
  - .squad/ → cwd subfolder (team state lives here)
- Add gentFileRoot option to InitOptions for explicit control
- Update team root resolution: check CWD first for .squad/, then
  fall back to git root (enables multiple squads per monorepo)

Closes #939

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 packages/squad-cli/src/cli/core/init.ts       | 28 +++++++++++--------
 .../templates/squad.agent.md.template         |  8 ++++--
 packages/squad-sdk/src/config/init.ts         |  7 ++++-
 .../templates/squad.agent.md.template         |  8 ++++--
 4 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/packages/squad-cli/src/cli/core/init.ts b/packages/squad-cli/src/cli/core/init.ts
index c0619dd21..effb8130b 100644
--- a/packages/squad-cli/src/cli/core/init.ts
+++ b/packages/squad-cli/src/cli/core/init.ts
@@ -123,10 +123,12 @@ export async function runInit(dest: string, options: RunInitOptions = {}): Promi
   // Detect project type
   const projectType = detectProjectType(dest);
 
-  // ── Parent git repo detection ─────────────────────────────────────
+  // ── Monorepo / subfolder detection ───────────────────────────────
   // Copilot resolves .github/agents/ relative to the git root.
-  // If CWD is inside a parent git repo, the agent file will be
-  // invisible to copilot because the git root points elsewhere.
+  // If CWD is a subfolder of a larger repo (monorepo), we place
+  // squad.agent.md at the git root and .squad/ in the subfolder.
+  // Never run `git init` — it creates broken nested repos (#939).
+  let agentFileRoot = dest; // default: place agent file relative to dest
   try {
     const gitRoot = execFileSync('git', ['rev-parse', '--show-toplevel'], {
       cwd: dest, encoding: 'utf-8', stdio: ['pipe', 'pipe', 'pipe'],
@@ -135,18 +137,19 @@ export async function runInit(dest: string, options: RunInitOptions = {}): Promi
     const normalGitRoot = path.resolve(gitRoot);
     if (normalDest.toLowerCase() !== normalGitRoot.toLowerCase()) {
       console.log();
-      console.log(`${YELLOW}${BOLD}⚠  Parent git repo detected${RESET}`);
-      console.log(`${YELLOW}   Git root:  ${normalGitRoot}${RESET}`);
-      console.log(`${YELLOW}   You're in: ${normalDest}${RESET}`);
+      console.log(`${CYAN}${BOLD}📦 Monorepo detected${RESET}`);
+      console.log(`${DIM}   Git root:  ${normalGitRoot}${RESET}`);
+      console.log(`${DIM}   You're in: ${normalDest}${RESET}`);
       console.log();
-      console.log(`${DIM}Copilot resolves .github/agents/ from the git root, not from here.${RESET}`);
-      console.log(`${DIM}The Squad agent won't be visible to copilot in this folder.${RESET}`);
-      console.log(`${DIM}Consider running squad init from the git root instead.${RESET}`);
+      console.log(`${DIM}squad.agent.md → git root (.github/agents/)${RESET}`);
+      console.log(`${DIM}.squad/        → here (${path.basename(normalDest)}/)${RESET}`);
       console.log();
+      // Place the agent file at the git root so Copilot can find it.
+      // Team state (.squad/) stays in cwd — resolved via cwd at runtime.
+      agentFileRoot = normalGitRoot;
     }
   } catch {
-    // No git available or not in a git repo — that's fine, continue normally.
-    // Copilot will fall back to CWD for .github/agents/ discovery.
+    // No git available or not in a git repo — continue normally.
   }
 
   // Detect squad directory
@@ -205,6 +208,7 @@ export async function runInit(dest: string, options: RunInitOptions = {}): Promi
   // Build SDK options
   const initOptions: InitOptions = {
     teamRoot: dest,
+    agentFileRoot,
     projectName: path.basename(dest) || 'my-project',
     agents: [
       {
@@ -255,7 +259,7 @@ export async function runInit(dest: string, options: RunInitOptions = {}): Promi
   process.off('SIGINT', sigintHandler);
 
   // Ensure version is fully stamped in squad.agent.md
-  const agentPath = path.join(dest, '.github', 'agents', 'squad.agent.md');
+  const agentPath = path.join(agentFileRoot, '.github', 'agents', 'squad.agent.md');
   if (storage.existsSync(agentPath)) {
     stampVersion(agentPath, version);
   }
diff --git a/packages/squad-cli/templates/squad.agent.md.template b/packages/squad-cli/templates/squad.agent.md.template
index c1d0a34e7..01e18dfad 100644
--- a/packages/squad-cli/templates/squad.agent.md.template
+++ b/packages/squad-cli/templates/squad.agent.md.template
@@ -625,15 +625,17 @@ Squad and all spawned agents may be running inside a **git worktree** rather tha
 
 **How the Coordinator resolves the team root (on every session start):**
 
-1. Run `git rev-parse --show-toplevel` to get the current worktree root.
-2. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
+1. **Check CWD first** — does `.squad/` exist in the current working directory?
+   - **Yes** → Team root = CWD. This handles monorepos where `.squad/` lives in a subfolder.
+2. If not, run `git rev-parse --show-toplevel` to get the current worktree root.
+3. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
    - **Yes** → use **worktree-local** strategy. Team root = current worktree root.
    - **No** → use **main-checkout** strategy. Discover the main working tree:
      ```
      git worktree list --porcelain
      ```
      The first `worktree` line is the main working tree. Team root = that path.
-3. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
+4. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
 
 **Passing the team root to agents:**
 - The Coordinator includes `TEAM_ROOT: {resolved_path}` in every spawn prompt.
diff --git a/packages/squad-sdk/src/config/init.ts b/packages/squad-sdk/src/config/init.ts
index 663fb74c1..9416d2a3b 100644
--- a/packages/squad-sdk/src/config/init.ts
+++ b/packages/squad-sdk/src/config/init.ts
@@ -136,6 +136,11 @@ export interface InitOptions {
   streams?: SubSquadDefinition[];
   /** If true, use built-in base roles with useRole() in SDK config (default: false) */
   roles?: boolean;
+  /** Root directory for the .github/agents/squad.agent.md file.
+   *  Defaults to teamRoot. In monorepos, this should be the git root
+   *  so Copilot can discover the agent file, while teamRoot stays in
+   *  the subfolder where .squad/ lives. */
+  agentFileRoot?: string;
   /** ADO work item configuration — used when platform is azure-devops */
   adoConfig?: {
     defaultWorkItemType?: string;
@@ -1062,7 +1067,7 @@ ${projectDescription ? `- **Description:** ${projectDescription}\n` : ''}- **Cre
   // Create .github/agents/squad.agent.md
   // -------------------------------------------------------------------------
   
-  const agentFile = join(teamRoot, '.github', 'agents', 'squad.agent.md');
+  const agentFile = join(options.agentFileRoot ?? teamRoot, '.github', 'agents', 'squad.agent.md');
   if (!storage.existsSync(agentFile) || !skipExisting) {
     if (templatesDir && storage.existsSync(join(templatesDir, 'squad.agent.md.template'))) {
       let agentContent = storage.readSync(join(templatesDir, 'squad.agent.md.template')) ?? '';
diff --git a/packages/squad-sdk/templates/squad.agent.md.template b/packages/squad-sdk/templates/squad.agent.md.template
index c1d0a34e7..01e18dfad 100644
--- a/packages/squad-sdk/templates/squad.agent.md.template
+++ b/packages/squad-sdk/templates/squad.agent.md.template
@@ -625,15 +625,17 @@ Squad and all spawned agents may be running inside a **git worktree** rather tha
 
 **How the Coordinator resolves the team root (on every session start):**
 
-1. Run `git rev-parse --show-toplevel` to get the current worktree root.
-2. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
+1. **Check CWD first** — does `.squad/` exist in the current working directory?
+   - **Yes** → Team root = CWD. This handles monorepos where `.squad/` lives in a subfolder.
+2. If not, run `git rev-parse --show-toplevel` to get the current worktree root.
+3. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
    - **Yes** → use **worktree-local** strategy. Team root = current worktree root.
    - **No** → use **main-checkout** strategy. Discover the main working tree:
      ```
      git worktree list --porcelain
      ```
      The first `worktree` line is the main working tree. Team root = that path.
-3. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
+4. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
 
 **Passing the team root to agents:**
 - The Coordinator includes `TEAM_ROOT: {resolved_path}` in every spawn prompt.

From 0017b07ff79254c75594e49bbeaba47c95b18894 Mon Sep 17 00:00:00 2001
From: Copilot <copilot@github.com>
Date: Thu, 9 Apr 2026 10:44:06 +0300
Subject: [PATCH 2/4] =?UTF-8?q?fix:=20address=20PR=20review=20feedback=20?=
 =?UTF-8?q?=E2=80=94=20template=20sync,=20tests,=20code=20reuse?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Sync canonical template (.squad-templates/) and run sync-templates.mjs
- Fix toRelativePath() to use path.relative() for cross-root paths
- Reuse detectParentGitRepo() instead of duplicating git-root logic
- Add monorepo regression test (no nested .git, agent at root, .squad in subfolder)
- Add .changeset for release tracking

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 .changeset/monorepo-subfolder-support.md |  8 ++++++
 .github/agents/squad.agent.md            |  8 +++---
 .squad-templates/squad.agent.md          |  8 +++---
 packages/squad-cli/src/cli/core/init.ts  | 34 +++++++++---------------
 packages/squad-sdk/src/config/init.ts    | 15 ++++-------
 templates/squad.agent.md.template        |  8 +++---
 test/init-scaffolding.test.ts            | 25 +++++++++++++++++
 7 files changed, 66 insertions(+), 40 deletions(-)
 create mode 100644 .changeset/monorepo-subfolder-support.md

diff --git a/.changeset/monorepo-subfolder-support.md b/.changeset/monorepo-subfolder-support.md
new file mode 100644
index 000000000..83eefed28
--- /dev/null
+++ b/.changeset/monorepo-subfolder-support.md
@@ -0,0 +1,8 @@
+---
+"@bradygaster/squad-cli": patch
+"@bradygaster/squad-sdk": patch
+---
+
+fix: monorepo subfolder support — never run git init (#939)
+
+When `squad init` runs in a subfolder of a monorepo, place `.github/agents/squad.agent.md` at the git root and `.squad/` in the subfolder. Never run `git init`.
diff --git a/.github/agents/squad.agent.md b/.github/agents/squad.agent.md
index c1d0a34e7..01e18dfad 100644
--- a/.github/agents/squad.agent.md
+++ b/.github/agents/squad.agent.md
@@ -625,15 +625,17 @@ Squad and all spawned agents may be running inside a **git worktree** rather tha
 
 **How the Coordinator resolves the team root (on every session start):**
 
-1. Run `git rev-parse --show-toplevel` to get the current worktree root.
-2. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
+1. **Check CWD first** — does `.squad/` exist in the current working directory?
+   - **Yes** → Team root = CWD. This handles monorepos where `.squad/` lives in a subfolder.
+2. If not, run `git rev-parse --show-toplevel` to get the current worktree root.
+3. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
    - **Yes** → use **worktree-local** strategy. Team root = current worktree root.
    - **No** → use **main-checkout** strategy. Discover the main working tree:
      ```
      git worktree list --porcelain
      ```
      The first `worktree` line is the main working tree. Team root = that path.
-3. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
+4. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
 
 **Passing the team root to agents:**
 - The Coordinator includes `TEAM_ROOT: {resolved_path}` in every spawn prompt.
diff --git a/.squad-templates/squad.agent.md b/.squad-templates/squad.agent.md
index c1d0a34e7..01e18dfad 100644
--- a/.squad-templates/squad.agent.md
+++ b/.squad-templates/squad.agent.md
@@ -625,15 +625,17 @@ Squad and all spawned agents may be running inside a **git worktree** rather tha
 
 **How the Coordinator resolves the team root (on every session start):**
 
-1. Run `git rev-parse --show-toplevel` to get the current worktree root.
-2. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
+1. **Check CWD first** — does `.squad/` exist in the current working directory?
+   - **Yes** → Team root = CWD. This handles monorepos where `.squad/` lives in a subfolder.
+2. If not, run `git rev-parse --show-toplevel` to get the current worktree root.
+3. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
    - **Yes** → use **worktree-local** strategy. Team root = current worktree root.
    - **No** → use **main-checkout** strategy. Discover the main working tree:
      ```
      git worktree list --porcelain
      ```
      The first `worktree` line is the main working tree. Team root = that path.
-3. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
+4. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
 
 **Passing the team root to agents:**
 - The Coordinator includes `TEAM_ROOT: {resolved_path}` in every spawn prompt.
diff --git a/packages/squad-cli/src/cli/core/init.ts b/packages/squad-cli/src/cli/core/init.ts
index effb8130b..abaefb19a 100644
--- a/packages/squad-cli/src/cli/core/init.ts
+++ b/packages/squad-cli/src/cli/core/init.ts
@@ -129,27 +129,19 @@ export async function runInit(dest: string, options: RunInitOptions = {}): Promi
   // squad.agent.md at the git root and .squad/ in the subfolder.
   // Never run `git init` — it creates broken nested repos (#939).
   let agentFileRoot = dest; // default: place agent file relative to dest
-  try {
-    const gitRoot = execFileSync('git', ['rev-parse', '--show-toplevel'], {
-      cwd: dest, encoding: 'utf-8', stdio: ['pipe', 'pipe', 'pipe'],
-    }).trim().replace(/\//g, path.sep);
-    const normalDest = path.resolve(dest);
-    const normalGitRoot = path.resolve(gitRoot);
-    if (normalDest.toLowerCase() !== normalGitRoot.toLowerCase()) {
-      console.log();
-      console.log(`${CYAN}${BOLD}📦 Monorepo detected${RESET}`);
-      console.log(`${DIM}   Git root:  ${normalGitRoot}${RESET}`);
-      console.log(`${DIM}   You're in: ${normalDest}${RESET}`);
-      console.log();
-      console.log(`${DIM}squad.agent.md → git root (.github/agents/)${RESET}`);
-      console.log(`${DIM}.squad/        → here (${path.basename(normalDest)}/)${RESET}`);
-      console.log();
-      // Place the agent file at the git root so Copilot can find it.
-      // Team state (.squad/) stays in cwd — resolved via cwd at runtime.
-      agentFileRoot = normalGitRoot;
-    }
-  } catch {
-    // No git available or not in a git repo — continue normally.
+  const parentGitRoot = detectParentGitRepo(dest);
+  if (parentGitRoot) {
+    console.log();
+    console.log(`${CYAN}${BOLD}📦 Monorepo detected${RESET}`);
+    console.log(`${DIM}   Git root:  ${parentGitRoot}${RESET}`);
+    console.log(`${DIM}   You're in: ${path.resolve(dest)}${RESET}`);
+    console.log();
+    console.log(`${DIM}squad.agent.md → git root (.github/agents/)${RESET}`);
+    console.log(`${DIM}.squad/        → here (${path.basename(path.resolve(dest))}/)${RESET}`);
+    console.log();
+    // Place the agent file at the git root so Copilot can find it.
+    // Team state (.squad/) stays in cwd — resolved via cwd at runtime.
+    agentFileRoot = parentGitRoot;
   }
 
   // Detect squad directory
diff --git a/packages/squad-sdk/src/config/init.ts b/packages/squad-sdk/src/config/init.ts
index 9416d2a3b..ec2983a72 100644
--- a/packages/squad-sdk/src/config/init.ts
+++ b/packages/squad-sdk/src/config/init.ts
@@ -8,7 +8,7 @@
  * @module config/init
  */
 
-import { join, dirname } from 'path';
+import { join, dirname, relative as pathRelative } from 'path';
 import { fileURLToPath } from 'url';
 import type { StorageProvider } from '../storage/index.js';
 import { FSStorageProvider } from '../storage/index.js';
@@ -674,15 +674,10 @@ export async function initSquad(options: InitOptions, storage: StorageProvider =
   
   // Helper to convert absolute path to relative
   const toRelativePath = (absolutePath: string): string => {
-    // Use path separator-agnostic approach
-    if (absolutePath.startsWith(teamRoot)) {
-      const relative = absolutePath.slice(teamRoot.length);
-      // Remove leading separator if present
-      return relative.startsWith('/') || relative.startsWith('\\') 
-        ? relative.slice(1) 
-        : relative;
-    }
-    return absolutePath;
+    // Use path.relative for correct cross-root handling (monorepo: agentFileRoot != teamRoot)
+    const rel = pathRelative(teamRoot, absolutePath);
+    // path.relative returns '' for same path, use '.' instead
+    return rel || '.';
   };
 
   // Helper to write file (respects skipExisting)
diff --git a/templates/squad.agent.md.template b/templates/squad.agent.md.template
index c1d0a34e7..01e18dfad 100644
--- a/templates/squad.agent.md.template
+++ b/templates/squad.agent.md.template
@@ -625,15 +625,17 @@ Squad and all spawned agents may be running inside a **git worktree** rather tha
 
 **How the Coordinator resolves the team root (on every session start):**
 
-1. Run `git rev-parse --show-toplevel` to get the current worktree root.
-2. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
+1. **Check CWD first** — does `.squad/` exist in the current working directory?
+   - **Yes** → Team root = CWD. This handles monorepos where `.squad/` lives in a subfolder.
+2. If not, run `git rev-parse --show-toplevel` to get the current worktree root.
+3. Check if `.squad/` exists at that root (fall back to `.ai-team/` for repos that haven't migrated yet).
    - **Yes** → use **worktree-local** strategy. Team root = current worktree root.
    - **No** → use **main-checkout** strategy. Discover the main working tree:
      ```
      git worktree list --porcelain
      ```
      The first `worktree` line is the main working tree. Team root = that path.
-3. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
+4. The user may override the strategy at any time (e.g., *"use main checkout for team state"* or *"keep team state in this worktree"*).
 
 **Passing the team root to agents:**
 - The Coordinator includes `TEAM_ROOT: {resolved_path}` in every spawn prompt.
diff --git a/test/init-scaffolding.test.ts b/test/init-scaffolding.test.ts
index c73411488..03da202db 100644
--- a/test/init-scaffolding.test.ts
+++ b/test/init-scaffolding.test.ts
@@ -223,6 +223,31 @@ describe('no-remote resilience (#579)', () => {
     await expect(initSquad(sdkOptions(TEST_ROOT))).resolves.toBeDefined();
     expect(existsSync(join(TEST_ROOT, '.squad', 'casting', 'registry.json'))).toBe(true);
   });
+
+  it('monorepo subfolder: no nested git init, agent at root, .squad in subfolder (#939)', async () => {
+    // Set up a monorepo with a subfolder
+    gitInit(TEST_ROOT);
+    const subfolder = join(TEST_ROOT, 'team-alpha');
+    await mkdir(subfolder, { recursive: true });
+
+    // Run SDK init with agentFileRoot pointing to the git root
+    const result = await initSquad({
+      ...sdkOptions(subfolder),
+      agentFileRoot: TEST_ROOT,
+    });
+
+    // 1. No nested .git/ in subfolder
+    expect(existsSync(join(subfolder, '.git'))).toBe(false);
+    // 2. .squad/ created in subfolder
+    expect(existsSync(join(subfolder, '.squad'))).toBe(true);
+    expect(existsSync(join(subfolder, '.squad', 'casting', 'registry.json'))).toBe(true);
+    // 3. squad.agent.md created at monorepo root
+    expect(existsSync(join(TEST_ROOT, '.github', 'agents', 'squad.agent.md'))).toBe(true);
+    // 4. squad.agent.md NOT in subfolder
+    expect(existsSync(join(subfolder, '.github', 'agents', 'squad.agent.md'))).toBe(false);
+    // 5. createdFiles should include relative path with ..
+    expect(result.createdFiles.some(f => f.includes('squad.agent.md'))).toBe(true);
+  });
 });
 
 // ─── Doctor validation after init ──────────────────────────────────────

From efe893bfb9b963bae81cf7c250bf25dbcf15edcf Mon Sep 17 00:00:00 2001
From: Copilot <copilot@github.com>
Date: Thu, 9 Apr 2026 12:39:29 +0300
Subject: [PATCH 3/4] fix: skip workflows in monorepo-subfolder mode (#939)

GitHub Actions only reads workflows from <repo-root>/.github/workflows/.
In monorepo mode, placing workflows in a subfolder has no effect.
Additionally, multiple squads would conflict on the same workflow files.

- Skip workflow placement when agentFileRoot != teamRoot
- Emit warning in InitResult.warnings explaining why
- Add workflow skip + warning assertions to monorepo test

Found by Q (Devil's Advocate reviewer) during E2E test review.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 .github/agents/squad.agent.md         | 4 ++--
 package.json                          | 2 +-
 packages/squad-cli/package.json       | 2 +-
 packages/squad-sdk/package.json       | 2 +-
 packages/squad-sdk/src/config/init.ts | 9 +++++++++
 test/init-scaffolding.test.ts         | 6 ++++++
 6 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/.github/agents/squad.agent.md b/.github/agents/squad.agent.md
index 01e18dfad..9dadbe7f1 100644
--- a/.github/agents/squad.agent.md
+++ b/.github/agents/squad.agent.md
@@ -3,14 +3,14 @@ name: Squad
 description: "Your AI team. Describe what you're building, get a team of specialists that live in your repo."
 ---
 
-<!-- version: 0.0.0-source -->
+<!-- version: 0.9.1-build.3 -->
 
 You are **Squad (Coordinator)** — the orchestrator for this project's AI team.
 
 ### Coordinator Identity
 
 - **Name:** Squad (Coordinator)
-- **Version:** 0.0.0-source (see HTML comment above — this value is stamped during install/upgrade). Include it as `Squad v{version}` in your first response of each session (e.g., in the acknowledgment or greeting).
+- **Version:** 0.9.1-build.3 (see HTML comment above — this value is stamped during install/upgrade). Include it as `Squad v0.9.1-build.3` in your first response of each session (e.g., in the acknowledgment or greeting).
 - **Role:** Agent orchestration, handoff enforcement, reviewer gating
 - **Inputs:** User request, repository state, `.squad/decisions.md`
 - **Outputs owned:** Final assembled artifacts, orchestration log (via Scribe)
diff --git a/package.json b/package.json
index c01bc0a6d..f3ba74257 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@bradygaster/squad",
-  "version": "0.9.1",
+  "version": "0.9.1-build.3",
   "private": true,
   "description": "Squad — Programmable multi-agent runtime for GitHub Copilot, built on @github/copilot-sdk",
   "type": "module",
diff --git a/packages/squad-cli/package.json b/packages/squad-cli/package.json
index e84fa7aa5..82ae944f6 100644
--- a/packages/squad-cli/package.json
+++ b/packages/squad-cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@bradygaster/squad-cli",
-  "version": "0.9.1",
+  "version": "0.9.1-build.3",
   "description": "Squad CLI — Command-line interface for the Squad multi-agent runtime",
   "type": "module",
   "bin": {
diff --git a/packages/squad-sdk/package.json b/packages/squad-sdk/package.json
index 3e9e3e184..fb9fed9f1 100644
--- a/packages/squad-sdk/package.json
+++ b/packages/squad-sdk/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@bradygaster/squad-sdk",
-  "version": "0.9.1",
+  "version": "0.9.1-build.3",
   "description": "Squad SDK — Programmable multi-agent runtime for GitHub Copilot",
   "type": "module",
   "main": "./dist/index.js",
diff --git a/packages/squad-sdk/src/config/init.ts b/packages/squad-sdk/src/config/init.ts
index ec2983a72..71add7f86 100644
--- a/packages/squad-sdk/src/config/init.ts
+++ b/packages/squad-sdk/src/config/init.ts
@@ -1110,6 +1110,14 @@ ${projectDescription ? `- **Description:** ${projectDescription}\n` : ''}- **Cre
   // -------------------------------------------------------------------------
   
   if (includeWorkflows && isGitHub && templatesDir && storage.existsSync(join(templatesDir, 'workflows'))) {
+    // In monorepo mode (agentFileRoot != teamRoot), skip workflow placement.
+    // GitHub Actions only reads from <repo-root>/.github/workflows/ — placing
+    // workflows in a subfolder has no effect. Multiple squads in one monorepo
+    // would also conflict on the same workflow files. (#939)
+    const isMonorepoSubfolder = options.agentFileRoot && options.agentFileRoot !== teamRoot;
+    if (isMonorepoSubfolder) {
+      warnings.push('Skipped GitHub Actions workflows in monorepo-subfolder mode — workflows must be at the git root. Set up workflows manually or use a single shared workflow for all squads.');
+    } else {
     const workflowsSrc = join(templatesDir, 'workflows');
     const workflowsDest = join(teamRoot, '.github', 'workflows');
     
@@ -1128,6 +1136,7 @@ ${projectDescription ? `- **Description:** ${projectDescription}\n` : ''}- **Cre
         }
       }
     }
+    }
   }
   
   // -------------------------------------------------------------------------
diff --git a/test/init-scaffolding.test.ts b/test/init-scaffolding.test.ts
index 03da202db..05988e314 100644
--- a/test/init-scaffolding.test.ts
+++ b/test/init-scaffolding.test.ts
@@ -231,9 +231,11 @@ describe('no-remote resilience (#579)', () => {
     await mkdir(subfolder, { recursive: true });
 
     // Run SDK init with agentFileRoot pointing to the git root
+    // Enable workflows to test monorepo skip behavior
     const result = await initSquad({
       ...sdkOptions(subfolder),
       agentFileRoot: TEST_ROOT,
+      includeWorkflows: true,
     });
 
     // 1. No nested .git/ in subfolder
@@ -247,6 +249,10 @@ describe('no-remote resilience (#579)', () => {
     expect(existsSync(join(subfolder, '.github', 'agents', 'squad.agent.md'))).toBe(false);
     // 5. createdFiles should include relative path with ..
     expect(result.createdFiles.some(f => f.includes('squad.agent.md'))).toBe(true);
+    // 6. Workflows NOT placed in subfolder (GitHub Actions ignores them there)
+    expect(existsSync(join(subfolder, '.github', 'workflows'))).toBe(false);
+    // 7. Warning emitted about skipped workflows
+    expect(result.warnings?.some(w => w.includes('monorepo-subfolder'))).toBe(true);
   });
 });
 

From 2a60095e610ff90c2419131df657f460cf12ade4 Mon Sep 17 00:00:00 2001
From: Copilot <copilot@github.com>
Date: Tue, 14 Apr 2026 09:19:20 +0300
Subject: [PATCH 4/4] =?UTF-8?q?fix:=20address=20review=20comments=20?=
 =?UTF-8?q?=E2=80=94=20revert=20build=20versions,=20path=20normalization,?=
 =?UTF-8?q?=20CLI=20test?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Revert all package.json versions from 0.9.1-build.3 to 0.9.1
  (build versions are local-only, changesets drive real bumps)
- Revert .github/agents/squad.agent.md to canonical template content
- Fix isMonorepoSubfolder: use path.resolve() + case-insensitive compare
- Add CLI-level runInit() monorepo test (verifies no .git in subfolder)
- Import path.resolve in SDK init.ts

Addresses review comments on #944.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 .github/agents/squad.agent.md         |  4 ++--
 package.json                          |  2 +-
 packages/squad-cli/package.json       |  2 +-
 packages/squad-sdk/package.json       |  2 +-
 packages/squad-sdk/src/config/init.ts |  5 +++--
 test/init-scaffolding.test.ts         | 19 +++++++++++++++++++
 6 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/.github/agents/squad.agent.md b/.github/agents/squad.agent.md
index 9dadbe7f1..01e18dfad 100644
--- a/.github/agents/squad.agent.md
+++ b/.github/agents/squad.agent.md
@@ -3,14 +3,14 @@ name: Squad
 description: "Your AI team. Describe what you're building, get a team of specialists that live in your repo."
 ---
 
-<!-- version: 0.9.1-build.3 -->
+<!-- version: 0.0.0-source -->
 
 You are **Squad (Coordinator)** — the orchestrator for this project's AI team.
 
 ### Coordinator Identity
 
 - **Name:** Squad (Coordinator)
-- **Version:** 0.9.1-build.3 (see HTML comment above — this value is stamped during install/upgrade). Include it as `Squad v0.9.1-build.3` in your first response of each session (e.g., in the acknowledgment or greeting).
+- **Version:** 0.0.0-source (see HTML comment above — this value is stamped during install/upgrade). Include it as `Squad v{version}` in your first response of each session (e.g., in the acknowledgment or greeting).
 - **Role:** Agent orchestration, handoff enforcement, reviewer gating
 - **Inputs:** User request, repository state, `.squad/decisions.md`
 - **Outputs owned:** Final assembled artifacts, orchestration log (via Scribe)
diff --git a/package.json b/package.json
index f3ba74257..c01bc0a6d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@bradygaster/squad",
-  "version": "0.9.1-build.3",
+  "version": "0.9.1",
   "private": true,
   "description": "Squad — Programmable multi-agent runtime for GitHub Copilot, built on @github/copilot-sdk",
   "type": "module",
diff --git a/packages/squad-cli/package.json b/packages/squad-cli/package.json
index 82ae944f6..e84fa7aa5 100644
--- a/packages/squad-cli/package.json
+++ b/packages/squad-cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@bradygaster/squad-cli",
-  "version": "0.9.1-build.3",
+  "version": "0.9.1",
   "description": "Squad CLI — Command-line interface for the Squad multi-agent runtime",
   "type": "module",
   "bin": {
diff --git a/packages/squad-sdk/package.json b/packages/squad-sdk/package.json
index fb9fed9f1..3e9e3e184 100644
--- a/packages/squad-sdk/package.json
+++ b/packages/squad-sdk/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@bradygaster/squad-sdk",
-  "version": "0.9.1-build.3",
+  "version": "0.9.1",
   "description": "Squad SDK — Programmable multi-agent runtime for GitHub Copilot",
   "type": "module",
   "main": "./dist/index.js",
diff --git a/packages/squad-sdk/src/config/init.ts b/packages/squad-sdk/src/config/init.ts
index 71add7f86..1533a3421 100644
--- a/packages/squad-sdk/src/config/init.ts
+++ b/packages/squad-sdk/src/config/init.ts
@@ -8,7 +8,7 @@
  * @module config/init
  */
 
-import { join, dirname, relative as pathRelative } from 'path';
+import { join, dirname, relative as pathRelative, resolve as pathResolve } from 'path';
 import { fileURLToPath } from 'url';
 import type { StorageProvider } from '../storage/index.js';
 import { FSStorageProvider } from '../storage/index.js';
@@ -1114,7 +1114,8 @@ ${projectDescription ? `- **Description:** ${projectDescription}\n` : ''}- **Cre
     // GitHub Actions only reads from <repo-root>/.github/workflows/ — placing
     // workflows in a subfolder has no effect. Multiple squads in one monorepo
     // would also conflict on the same workflow files. (#939)
-    const isMonorepoSubfolder = options.agentFileRoot && options.agentFileRoot !== teamRoot;
+    const isMonorepoSubfolder = !!options.agentFileRoot &&
+      pathResolve(options.agentFileRoot).toLowerCase() !== pathResolve(teamRoot).toLowerCase();
     if (isMonorepoSubfolder) {
       warnings.push('Skipped GitHub Actions workflows in monorepo-subfolder mode — workflows must be at the git root. Set up workflows manually or use a single shared workflow for all squads.');
     } else {
diff --git a/test/init-scaffolding.test.ts b/test/init-scaffolding.test.ts
index 05988e314..3b180a812 100644
--- a/test/init-scaffolding.test.ts
+++ b/test/init-scaffolding.test.ts
@@ -218,6 +218,25 @@ describe('no-remote resilience (#579)', () => {
     expect(existsSync(join(TEST_ROOT, '.github', 'agents', 'squad.agent.md'))).toBe(true);
   });
 
+  it('runInit CLI: monorepo subfolder — no nested .git, agent at git root (#939)', async () => {
+    // Set up a monorepo: git init at TEST_ROOT, run from a subfolder
+    gitInit(TEST_ROOT);
+    const subfolder = join(TEST_ROOT, 'services', 'api');
+    await mkdir(subfolder, { recursive: true });
+
+    // runInit from the subfolder — CLI should detect the parent git repo
+    await expect(runInit(subfolder)).resolves.toBeUndefined();
+
+    // 1. No nested .git/ in subfolder (the original bug)
+    expect(existsSync(join(subfolder, '.git'))).toBe(false);
+    // 2. .squad/ created in the subfolder
+    expect(existsSync(join(subfolder, '.squad'))).toBe(true);
+    expect(existsSync(join(subfolder, '.squad', 'casting', 'registry.json'))).toBe(true);
+    // 3. squad.agent.md placed at the git root, not the subfolder
+    expect(existsSync(join(TEST_ROOT, '.github', 'agents', 'squad.agent.md'))).toBe(true);
+    expect(existsSync(join(subfolder, '.github', 'agents', 'squad.agent.md'))).toBe(false);
+  });
+
   it('initSquad succeeds when git is not initialized at all', async () => {
     // TEST_ROOT is a plain directory — no git init
     await expect(initSquad(sdkOptions(TEST_ROOT))).resolves.toBeDefined();