Merge PR #654: feat: git worktree isolation for parallel CLI sessions (--worktree / -w)

Adds --worktree (-w) flag to hermes CLI for isolated git worktree sessions.
Multiple agents can work on the same repo concurrently without collisions.

Closes #652

AGENTS.md

@@ -226,6 +226,7 @@ The unified `hermes` command provides all functionality:
 |---------|-------------|
 | `hermes` | Interactive chat (default) |
 | `hermes chat -q "..."` | Single query mode |
+| `hermes -w` / `hermes --worktree` | Start in isolated git worktree (for parallel agents) |
 | `hermes setup` | Configure API keys and settings |
 | `hermes config` | View current configuration |
 | `hermes config edit` | Open config in editor |

cli-config.yaml.example

@@ -50,6 +50,16 @@ model:
 #   # Data policy: "allow" (default) or "deny" to exclude providers that may store data
 #   # data_collection: "deny"
 
+# =============================================================================
+# Git Worktree Isolation
+# =============================================================================
+# When enabled, each CLI session creates an isolated git worktree so multiple
+# agents can work on the same repo concurrently without file collisions.
+# Equivalent to always passing --worktree / -w on the command line.
+#
+# worktree: true    # Always create a worktree when in a git repo
+# worktree: false   # Default — only create when -w flag is passed
+
 # =============================================================================
 # Terminal Tool Configuration
 # =============================================================================

cli.py

@@ -395,6 +395,227 @@ def _run_cleanup():
     except Exception:
         pass
 
+
+# =============================================================================
+# Git Worktree Isolation (#652)
+# =============================================================================
+
+# Tracks the active worktree for cleanup on exit
+_active_worktree: Optional[Dict[str, str]] = None
+
+
+def _git_repo_root() -> Optional[str]:
+    """Return the git repo root for CWD, or None if not in a repo."""
+    import subprocess
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--show-toplevel"],
+            capture_output=True, text=True, timeout=5,
+        )
+        if result.returncode == 0:
+            return result.stdout.strip()
+    except Exception:
+        pass
+    return None
+
+
+def _setup_worktree(repo_root: str = None) -> Optional[Dict[str, str]]:
+    """Create an isolated git worktree for this CLI session.
+
+    Returns a dict with worktree metadata on success, None on failure.
+    The dict contains: path, branch, repo_root.
+    """
+    import subprocess
+
+    repo_root = repo_root or _git_repo_root()
+    if not repo_root:
+        print("\033[33m⚠ --worktree: not inside a git repository, skipping.\033[0m")
+        return None
+
+    short_id = uuid.uuid4().hex[:8]
+    wt_name = f"hermes-{short_id}"
+    branch_name = f"hermes/{wt_name}"
+
+    worktrees_dir = Path(repo_root) / ".worktrees"
+    worktrees_dir.mkdir(parents=True, exist_ok=True)
+
+    wt_path = worktrees_dir / wt_name
+
+    # Ensure .worktrees/ is in .gitignore
+    gitignore = Path(repo_root) / ".gitignore"
+    _ignore_entry = ".worktrees/"
+    try:
+        existing = gitignore.read_text() if gitignore.exists() else ""
+        if _ignore_entry not in existing.splitlines():
+            with open(gitignore, "a") as f:
+                if existing and not existing.endswith("\n"):
+                    f.write("\n")
+                f.write(f"{_ignore_entry}\n")
+    except Exception as e:
+        logger.debug("Could not update .gitignore: %s", e)
+
+    # Create the worktree
+    try:
+        result = subprocess.run(
+            ["git", "worktree", "add", str(wt_path), "-b", branch_name, "HEAD"],
+            capture_output=True, text=True, timeout=30, cwd=repo_root,
+        )
+        if result.returncode != 0:
+            print(f"\033[31m✗ Failed to create worktree: {result.stderr.strip()}\033[0m")
+            return None
+    except Exception as e:
+        print(f"\033[31m✗ Failed to create worktree: {e}\033[0m")
+        return None
+
+    # Copy files listed in .worktreeinclude (gitignored files the agent needs)
+    include_file = Path(repo_root) / ".worktreeinclude"
+    if include_file.exists():
+        try:
+            for line in include_file.read_text().splitlines():
+                entry = line.strip()
+                if not entry or entry.startswith("#"):
+                    continue
+                src = Path(repo_root) / entry
+                dst = wt_path / entry
+                if src.is_file():
+                    dst.parent.mkdir(parents=True, exist_ok=True)
+                    shutil.copy2(str(src), str(dst))
+                elif src.is_dir():
+                    # Symlink directories (faster, saves disk)
+                    if not dst.exists():
+                        dst.parent.mkdir(parents=True, exist_ok=True)
+                        os.symlink(str(src.resolve()), str(dst))
+        except Exception as e:
+            logger.debug("Error copying .worktreeinclude entries: %s", e)
+
+    info = {
+        "path": str(wt_path),
+        "branch": branch_name,
+        "repo_root": repo_root,
+    }
+
+    print(f"\033[32m✓ Worktree created:\033[0m {wt_path}")
+    print(f"  Branch: {branch_name}")
+
+    return info
+
+
+def _cleanup_worktree(info: Dict[str, str] = None) -> None:
+    """Remove a worktree and its branch on exit.
+
+    If the worktree has uncommitted changes, warn and keep it.
+    """
+    global _active_worktree
+    info = info or _active_worktree
+    if not info:
+        return
+
+    import subprocess
+
+    wt_path = info["path"]
+    branch = info["branch"]
+    repo_root = info["repo_root"]
+
+    if not Path(wt_path).exists():
+        return
+
+    # Check for uncommitted changes
+    try:
+        status = subprocess.run(
+            ["git", "status", "--porcelain"],
+            capture_output=True, text=True, timeout=10, cwd=wt_path,
+        )
+        has_changes = bool(status.stdout.strip())
+    except Exception:
+        has_changes = True  # Assume dirty on error — don't delete
+
+    if has_changes:
+        print(f"\n\033[33m⚠ Worktree has uncommitted changes, keeping: {wt_path}\033[0m")
+        print(f"  To clean up manually: git worktree remove {wt_path}")
+        _active_worktree = None
+        return
+
+    # Remove worktree
+    try:
+        subprocess.run(
+            ["git", "worktree", "remove", wt_path, "--force"],
+            capture_output=True, text=True, timeout=15, cwd=repo_root,
+        )
+    except Exception as e:
+        logger.debug("Failed to remove worktree: %s", e)
+
+    # Delete the branch (only if it was never pushed / has no upstream)
+    try:
+        subprocess.run(
+            ["git", "branch", "-D", branch],
+            capture_output=True, text=True, timeout=10, cwd=repo_root,
+        )
+    except Exception as e:
+        logger.debug("Failed to delete branch %s: %s", branch, e)
+
+    _active_worktree = None
+    print(f"\033[32m✓ Worktree cleaned up: {wt_path}\033[0m")
+
+
+def _prune_stale_worktrees(repo_root: str, max_age_hours: int = 24) -> None:
+    """Remove worktrees older than max_age_hours that have no uncommitted changes.
+
+    Runs silently on startup to clean up after crashed/killed sessions.
+    """
+    import subprocess
+    import time
+
+    worktrees_dir = Path(repo_root) / ".worktrees"
+    if not worktrees_dir.exists():
+        return
+
+    now = time.time()
+    cutoff = now - (max_age_hours * 3600)
+
+    for entry in worktrees_dir.iterdir():
+        if not entry.is_dir() or not entry.name.startswith("hermes-"):
+            continue
+
+        # Check age
+        try:
+            mtime = entry.stat().st_mtime
+            if mtime > cutoff:
+                continue  # Too recent — skip
+        except Exception:
+            continue
+
+        # Check for uncommitted changes
+        try:
+            status = subprocess.run(
+                ["git", "status", "--porcelain"],
+                capture_output=True, text=True, timeout=5, cwd=str(entry),
+            )
+            if status.stdout.strip():
+                continue  # Has changes — skip
+        except Exception:
+            continue  # Can't check — skip
+
+        # Safe to remove
+        try:
+            branch_result = subprocess.run(
+                ["git", "branch", "--show-current"],
+                capture_output=True, text=True, timeout=5, cwd=str(entry),
+            )
+            branch = branch_result.stdout.strip()
+
+            subprocess.run(
+                ["git", "worktree", "remove", str(entry), "--force"],
+                capture_output=True, text=True, timeout=15, cwd=repo_root,
+            )
+            if branch:
+                subprocess.run(
+                    ["git", "branch", "-D", branch],
+                    capture_output=True, text=True, timeout=10, cwd=repo_root,
+                )
+            logger.debug("Pruned stale worktree: %s", entry.name)
+        except Exception as e:
+            logger.debug("Failed to prune worktree %s: %s", entry.name, e)
+
 # ============================================================================
 # ASCII Art & Branding
 # ============================================================================
@@ -3253,6 +3474,8 @@ def main(
     list_toolsets: bool = False,
     gateway: bool = False,
     resume: str = None,
+    worktree: bool = False,
+    w: bool = False,
 ):
     """
     Hermes Agent CLI - Interactive AI Assistant
@@ -3271,6 +3494,8 @@ def main(
         list_tools: List available tools and exit
         list_toolsets: List available toolsets and exit
         resume: Resume a previous session by its ID (e.g., 20260225_143052_a1b2c3)
+        worktree: Run in an isolated git worktree (for parallel agents). Alias: -w
+        w: Shorthand for --worktree
     
     Examples:
         python cli.py                            # Start interactive mode
@@ -3278,7 +3503,11 @@ def main(
         python cli.py -q "What is Python?"       # Single query mode
         python cli.py --list-tools               # List tools and exit
         python cli.py --resume 20260225_143052_a1b2c3  # Resume session
+        python cli.py -w                         # Start in isolated git worktree
+        python cli.py -w -q "Fix issue #123"     # Single query in worktree
     """
+    global _active_worktree
+
     # Signal to terminal_tool that we're in interactive mode
     # This enables interactive sudo password prompts with timeout
     os.environ["HERMES_INTERACTIVE"] = "1"
@@ -3290,6 +3519,26 @@ def main(
         print("Starting Hermes Gateway (messaging platforms)...")
         asyncio.run(start_gateway())
         return
+
+    # Skip worktree for list commands (they exit immediately)
+    if not list_tools and not list_toolsets:
+        # ── Git worktree isolation (#652) ──
+        # Create an isolated worktree so this agent instance doesn't collide
+        # with other agents working on the same repo.
+        use_worktree = worktree or w or CLI_CONFIG.get("worktree", False)
+        wt_info = None
+        if use_worktree:
+            # Prune stale worktrees from crashed/killed sessions
+            _repo = _git_repo_root()
+            if _repo:
+                _prune_stale_worktrees(_repo)
+            wt_info = _setup_worktree()
+            if wt_info:
+                _active_worktree = wt_info
+                os.environ["TERMINAL_CWD"] = wt_info["path"]
+                atexit.register(_cleanup_worktree, wt_info)
+    else:
+        wt_info = None
     
     # Handle query shorthand
     query = query or q
@@ -3328,6 +3577,17 @@ def main(
         compact=compact,
         resume=resume,
     )
+
+    # Inject worktree context into agent's system prompt
+    if wt_info:
+        wt_note = (
+            f"\n\n[System note: You are working in an isolated git worktree at "
+            f"{wt_info['path']}. Your branch is `{wt_info['branch']}`. "
+            f"Changes here do not affect the main working tree or other agents. "
+            f"Remember to commit and push your changes, and create a PR if appropriate. "
+            f"The original repo is at {wt_info['repo_root']}.]"
+        )
+        cli.system_prompt = (cli.system_prompt or "") + wt_note
     
     # Handle list commands (don't init agent for these)
     if list_tools:

hermes_cli/main.py

@@ -167,6 +167,7 @@ def cmd_chat(args):
         "verbose": args.verbose,
         "query": args.query,
         "resume": getattr(args, "resume", None),
+        "worktree": getattr(args, "worktree", False),
     }
     # Filter out None values
     kwargs = {k: v for k, v in kwargs.items() if v is not None}
@@ -1217,6 +1218,7 @@ Examples:
     hermes config edit            Edit config in $EDITOR
     hermes config set model gpt-4 Set a config value
     hermes gateway                Run messaging gateway
+    hermes -w                     Start in isolated git worktree
     hermes gateway install        Install as system service
     hermes sessions list          List past sessions
     hermes update                 Update to latest version
@@ -1244,6 +1246,12 @@ For more help on a command:
         default=False,
         help="Resume the most recent CLI session"
     )
+    parser.add_argument(
+        "--worktree", "-w",
+        action="store_true",
+        default=False,
+        help="Run in an isolated git worktree (for parallel agents)"
+    )
     
     subparsers = parser.add_subparsers(dest="command", help="Command to run")
     
@@ -1290,6 +1298,12 @@ For more help on a command:
         default=False,
         help="Resume the most recent CLI session"
     )
+    chat_parser.add_argument(
+        "--worktree", "-w",
+        action="store_true",
+        default=False,
+        help="Run in an isolated git worktree (for parallel agents on the same repo)"
+    )
     chat_parser.set_defaults(func=cmd_chat)
 
     # =========================================================================
@@ -1850,6 +1864,8 @@ For more help on a command:
         args.provider = None
         args.toolsets = None
         args.verbose = False
+        if not hasattr(args, "worktree"):
+            args.worktree = False
         cmd_chat(args)
         return
     
@@ -1862,6 +1878,8 @@ For more help on a command:
         args.verbose = False
         args.resume = None
         args.continue_last = False
+        if not hasattr(args, "worktree"):
+            args.worktree = False
         cmd_chat(args)
         return
     

tests/test_worktree.py

@@ -0,0 +1,635 @@
+"""Tests for git worktree isolation (CLI --worktree / -w flag).
+
+Verifies worktree creation, cleanup, .worktreeinclude handling,
+.gitignore management, and integration with the CLI.  (#652)
+"""
+
+import os
+import shutil
+import subprocess
+import pytest
+from pathlib import Path
+from unittest.mock import patch, MagicMock
+
+
+@pytest.fixture
+def git_repo(tmp_path):
+    """Create a temporary git repo for testing."""
+    repo = tmp_path / "test-repo"
+    repo.mkdir()
+    subprocess.run(["git", "init"], cwd=repo, capture_output=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@test.com"],
+        cwd=repo, capture_output=True,
+    )
+    subprocess.run(
+        ["git", "config", "user.name", "Test"],
+        cwd=repo, capture_output=True,
+    )
+    # Create initial commit (worktrees need at least one commit)
+    (repo / "README.md").write_text("# Test Repo\n")
+    subprocess.run(["git", "add", "."], cwd=repo, capture_output=True)
+    subprocess.run(
+        ["git", "commit", "-m", "Initial commit"],
+        cwd=repo, capture_output=True,
+    )
+    return repo
+
+
+# ---------------------------------------------------------------------------
+# Lightweight reimplementations for testing (avoid importing cli.py)
+# ---------------------------------------------------------------------------
+
+def _git_repo_root(cwd=None):
+    """Test version of _git_repo_root."""
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--show-toplevel"],
+            capture_output=True, text=True, timeout=5,
+            cwd=cwd,
+        )
+        if result.returncode == 0:
+            return result.stdout.strip()
+    except Exception:
+        pass
+    return None
+
+
+def _setup_worktree(repo_root):
+    """Test version of _setup_worktree — creates a worktree."""
+    import uuid
+    short_id = uuid.uuid4().hex[:8]
+    wt_name = f"hermes-{short_id}"
+    branch_name = f"hermes/{wt_name}"
+
+    worktrees_dir = Path(repo_root) / ".worktrees"
+    worktrees_dir.mkdir(parents=True, exist_ok=True)
+    wt_path = worktrees_dir / wt_name
+
+    result = subprocess.run(
+        ["git", "worktree", "add", str(wt_path), "-b", branch_name, "HEAD"],
+        capture_output=True, text=True, timeout=30, cwd=repo_root,
+    )
+    if result.returncode != 0:
+        return None
+
+    return {
+        "path": str(wt_path),
+        "branch": branch_name,
+        "repo_root": repo_root,
+    }
+
+
+def _cleanup_worktree(info):
+    """Test version of _cleanup_worktree."""
+    wt_path = info["path"]
+    branch = info["branch"]
+    repo_root = info["repo_root"]
+
+    if not Path(wt_path).exists():
+        return
+
+    # Check for uncommitted changes
+    status = subprocess.run(
+        ["git", "status", "--porcelain"],
+        capture_output=True, text=True, timeout=10, cwd=wt_path,
+    )
+    has_changes = bool(status.stdout.strip())
+
+    if has_changes:
+        return False  # Did not clean up
+
+    subprocess.run(
+        ["git", "worktree", "remove", wt_path, "--force"],
+        capture_output=True, text=True, timeout=15, cwd=repo_root,
+    )
+    subprocess.run(
+        ["git", "branch", "-D", branch],
+        capture_output=True, text=True, timeout=10, cwd=repo_root,
+    )
+    return True  # Cleaned up
+
+
+# ---------------------------------------------------------------------------
+# Tests
+# ---------------------------------------------------------------------------
+
+class TestGitRepoDetection:
+    """Test git repo root detection."""
+
+    def test_detects_git_repo(self, git_repo):
+        root = _git_repo_root(cwd=str(git_repo))
+        assert root is not None
+        assert Path(root).resolve() == git_repo.resolve()
+
+    def test_detects_subdirectory(self, git_repo):
+        subdir = git_repo / "src" / "lib"
+        subdir.mkdir(parents=True)
+        root = _git_repo_root(cwd=str(subdir))
+        assert root is not None
+        assert Path(root).resolve() == git_repo.resolve()
+
+    def test_returns_none_outside_repo(self, tmp_path):
+        # tmp_path itself is not a git repo
+        bare_dir = tmp_path / "not-a-repo"
+        bare_dir.mkdir()
+        root = _git_repo_root(cwd=str(bare_dir))
+        assert root is None
+
+
+class TestWorktreeCreation:
+    """Test worktree setup."""
+
+    def test_creates_worktree(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert Path(info["path"]).exists()
+        assert info["branch"].startswith("hermes/hermes-")
+        assert info["repo_root"] == str(git_repo)
+
+        # Verify it's a valid git worktree
+        result = subprocess.run(
+            ["git", "rev-parse", "--is-inside-work-tree"],
+            capture_output=True, text=True, cwd=info["path"],
+        )
+        assert result.stdout.strip() == "true"
+
+    def test_worktree_has_own_branch(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Check branch name in worktree
+        result = subprocess.run(
+            ["git", "branch", "--show-current"],
+            capture_output=True, text=True, cwd=info["path"],
+        )
+        assert result.stdout.strip() == info["branch"]
+
+    def test_worktree_is_independent(self, git_repo):
+        """Two worktrees from the same repo are independent."""
+        info1 = _setup_worktree(str(git_repo))
+        info2 = _setup_worktree(str(git_repo))
+        assert info1 is not None
+        assert info2 is not None
+        assert info1["path"] != info2["path"]
+        assert info1["branch"] != info2["branch"]
+
+        # Create a file in worktree 1
+        (Path(info1["path"]) / "only-in-wt1.txt").write_text("hello")
+
+        # It should NOT appear in worktree 2
+        assert not (Path(info2["path"]) / "only-in-wt1.txt").exists()
+
+    def test_worktrees_dir_created(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert (git_repo / ".worktrees").is_dir()
+
+    def test_worktree_has_repo_files(self, git_repo):
+        """Worktree should contain the repo's tracked files."""
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert (Path(info["path"]) / "README.md").exists()
+
+
+class TestWorktreeCleanup:
+    """Test worktree cleanup on exit."""
+
+    def test_clean_worktree_removed(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert Path(info["path"]).exists()
+
+        result = _cleanup_worktree(info)
+        assert result is True
+        assert not Path(info["path"]).exists()
+
+    def test_dirty_worktree_kept(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Make uncommitted changes
+        (Path(info["path"]) / "new-file.txt").write_text("uncommitted")
+        subprocess.run(
+            ["git", "add", "new-file.txt"],
+            cwd=info["path"], capture_output=True,
+        )
+
+        result = _cleanup_worktree(info)
+        assert result is False
+        assert Path(info["path"]).exists()  # Still there
+
+    def test_branch_deleted_on_cleanup(self, git_repo):
+        info = _setup_worktree(str(git_repo))
+        branch = info["branch"]
+
+        _cleanup_worktree(info)
+
+        # Branch should be gone
+        result = subprocess.run(
+            ["git", "branch", "--list", branch],
+            capture_output=True, text=True, cwd=str(git_repo),
+        )
+        assert branch not in result.stdout
+
+    def test_cleanup_nonexistent_worktree(self, git_repo):
+        """Cleanup should handle already-removed worktrees gracefully."""
+        info = {
+            "path": str(git_repo / ".worktrees" / "nonexistent"),
+            "branch": "hermes/nonexistent",
+            "repo_root": str(git_repo),
+        }
+        # Should not raise
+        _cleanup_worktree(info)
+
+
+class TestWorktreeInclude:
+    """Test .worktreeinclude file handling."""
+
+    def test_copies_included_files(self, git_repo):
+        """Files listed in .worktreeinclude should be copied to the worktree."""
+        # Create a .env file (gitignored)
+        (git_repo / ".env").write_text("SECRET=abc123")
+        (git_repo / ".gitignore").write_text(".env\n.worktrees/\n")
+        subprocess.run(
+            ["git", "add", ".gitignore"],
+            cwd=str(git_repo), capture_output=True,
+        )
+        subprocess.run(
+            ["git", "commit", "-m", "Add gitignore"],
+            cwd=str(git_repo), capture_output=True,
+        )
+
+        # Create .worktreeinclude
+        (git_repo / ".worktreeinclude").write_text(".env\n")
+
+        # Import and use the real _setup_worktree logic for include handling
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Manually copy .worktreeinclude entries (mirrors cli.py logic)
+        import shutil
+        include_file = git_repo / ".worktreeinclude"
+        wt_path = Path(info["path"])
+        for line in include_file.read_text().splitlines():
+            entry = line.strip()
+            if not entry or entry.startswith("#"):
+                continue
+            src = git_repo / entry
+            dst = wt_path / entry
+            if src.is_file():
+                dst.parent.mkdir(parents=True, exist_ok=True)
+                shutil.copy2(str(src), str(dst))
+
+        # Verify .env was copied
+        assert (wt_path / ".env").exists()
+        assert (wt_path / ".env").read_text() == "SECRET=abc123"
+
+    def test_ignores_comments_and_blanks(self, git_repo):
+        """Comments and blank lines in .worktreeinclude should be skipped."""
+        (git_repo / ".worktreeinclude").write_text(
+            "# This is a comment\n"
+            "\n"
+            "  # Another comment\n"
+        )
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        # Should not crash — just skip all lines
+
+
+class TestGitignoreManagement:
+    """Test that .worktrees/ is added to .gitignore."""
+
+    def test_adds_to_gitignore(self, git_repo):
+        """Creating a worktree should add .worktrees/ to .gitignore."""
+        # Remove any existing .gitignore
+        gitignore = git_repo / ".gitignore"
+        if gitignore.exists():
+            gitignore.unlink()
+
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Now manually add .worktrees/ to .gitignore (mirrors cli.py logic)
+        _ignore_entry = ".worktrees/"
+        existing = gitignore.read_text() if gitignore.exists() else ""
+        if _ignore_entry not in existing.splitlines():
+            with open(gitignore, "a") as f:
+                if existing and not existing.endswith("\n"):
+                    f.write("\n")
+                f.write(f"{_ignore_entry}\n")
+
+        content = gitignore.read_text()
+        assert ".worktrees/" in content
+
+    def test_does_not_duplicate_gitignore_entry(self, git_repo):
+        """If .worktrees/ is already in .gitignore, don't add again."""
+        gitignore = git_repo / ".gitignore"
+        gitignore.write_text(".worktrees/\n")
+
+        # The check should see it's already there
+        existing = gitignore.read_text()
+        assert ".worktrees/" in existing.splitlines()
+
+
+class TestMultipleWorktrees:
+    """Test running multiple worktrees concurrently (the core use case)."""
+
+    def test_ten_concurrent_worktrees(self, git_repo):
+        """Create 10 worktrees — simulating 10 parallel agents."""
+        worktrees = []
+        for _ in range(10):
+            info = _setup_worktree(str(git_repo))
+            assert info is not None
+            worktrees.append(info)
+
+        # All should exist and be independent
+        paths = [info["path"] for info in worktrees]
+        assert len(set(paths)) == 10  # All unique
+
+        # Each should have the repo files
+        for info in worktrees:
+            assert (Path(info["path"]) / "README.md").exists()
+
+        # Edit a file in one worktree
+        (Path(worktrees[0]["path"]) / "README.md").write_text("Modified in wt0")
+
+        # Others should be unaffected
+        for info in worktrees[1:]:
+            assert (Path(info["path"]) / "README.md").read_text() == "# Test Repo\n"
+
+        # List worktrees via git
+        result = subprocess.run(
+            ["git", "worktree", "list"],
+            capture_output=True, text=True, cwd=str(git_repo),
+        )
+        # Should have 11 entries: main + 10 worktrees
+        lines = [l for l in result.stdout.strip().splitlines() if l.strip()]
+        assert len(lines) == 11
+
+        # Cleanup all
+        for info in worktrees:
+            # Discard changes first so cleanup works
+            subprocess.run(
+                ["git", "checkout", "--", "."],
+                cwd=info["path"], capture_output=True,
+            )
+            _cleanup_worktree(info)
+
+        # All should be removed
+        for info in worktrees:
+            assert not Path(info["path"]).exists()
+
+
+class TestWorktreeDirectorySymlink:
+    """Test .worktreeinclude with directories (symlinked)."""
+
+    def test_symlinks_directory(self, git_repo):
+        """Directories in .worktreeinclude should be symlinked."""
+        # Create a .venv directory
+        venv_dir = git_repo / ".venv" / "lib"
+        venv_dir.mkdir(parents=True)
+        (venv_dir / "marker.txt").write_text("venv marker")
+        (git_repo / ".gitignore").write_text(".venv/\n.worktrees/\n")
+        subprocess.run(
+            ["git", "add", ".gitignore"], cwd=str(git_repo), capture_output=True
+        )
+        subprocess.run(
+            ["git", "commit", "-m", "gitignore"], cwd=str(git_repo), capture_output=True
+        )
+
+        (git_repo / ".worktreeinclude").write_text(".venv/\n")
+
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        wt_path = Path(info["path"])
+        src = git_repo / ".venv"
+        dst = wt_path / ".venv"
+
+        # Manually symlink (mirrors cli.py logic)
+        if not dst.exists():
+            dst.parent.mkdir(parents=True, exist_ok=True)
+            os.symlink(str(src.resolve()), str(dst))
+
+        assert dst.is_symlink()
+        assert (dst / "lib" / "marker.txt").read_text() == "venv marker"
+
+
+class TestStaleWorktreePruning:
+    """Test _prune_stale_worktrees garbage collection."""
+
+    def test_prunes_old_clean_worktree(self, git_repo):
+        """Old clean worktrees should be removed on prune."""
+        import time
+
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert Path(info["path"]).exists()
+
+        # Make the worktree look old (set mtime to 25h ago)
+        old_time = time.time() - (25 * 3600)
+        os.utime(info["path"], (old_time, old_time))
+
+        # Reimplementation of prune logic (matches cli.py)
+        worktrees_dir = git_repo / ".worktrees"
+        cutoff = time.time() - (24 * 3600)
+
+        for entry in worktrees_dir.iterdir():
+            if not entry.is_dir() or not entry.name.startswith("hermes-"):
+                continue
+            try:
+                mtime = entry.stat().st_mtime
+                if mtime > cutoff:
+                    continue
+            except Exception:
+                continue
+
+            status = subprocess.run(
+                ["git", "status", "--porcelain"],
+                capture_output=True, text=True, timeout=5, cwd=str(entry),
+            )
+            if status.stdout.strip():
+                continue
+
+            branch_result = subprocess.run(
+                ["git", "branch", "--show-current"],
+                capture_output=True, text=True, timeout=5, cwd=str(entry),
+            )
+            branch = branch_result.stdout.strip()
+            subprocess.run(
+                ["git", "worktree", "remove", str(entry), "--force"],
+                capture_output=True, text=True, timeout=15, cwd=str(git_repo),
+            )
+            if branch:
+                subprocess.run(
+                    ["git", "branch", "-D", branch],
+                    capture_output=True, text=True, timeout=10, cwd=str(git_repo),
+                )
+
+        assert not Path(info["path"]).exists()
+
+    def test_keeps_recent_worktree(self, git_repo):
+        """Recent worktrees should NOT be pruned."""
+        import time
+
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Don't modify mtime — it's recent
+        worktrees_dir = git_repo / ".worktrees"
+        cutoff = time.time() - (24 * 3600)
+
+        pruned = False
+        for entry in worktrees_dir.iterdir():
+            if not entry.is_dir() or not entry.name.startswith("hermes-"):
+                continue
+            mtime = entry.stat().st_mtime
+            if mtime > cutoff:
+                continue  # Too recent
+            pruned = True
+
+        assert not pruned
+        assert Path(info["path"]).exists()
+
+    def test_keeps_dirty_old_worktree(self, git_repo):
+        """Old worktrees with uncommitted changes should NOT be pruned."""
+        import time
+
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # Make it dirty
+        (Path(info["path"]) / "dirty.txt").write_text("uncommitted")
+        subprocess.run(
+            ["git", "add", "dirty.txt"],
+            cwd=info["path"], capture_output=True,
+        )
+
+        # Make it old
+        old_time = time.time() - (25 * 3600)
+        os.utime(info["path"], (old_time, old_time))
+
+        # Check if it would be pruned
+        status = subprocess.run(
+            ["git", "status", "--porcelain"],
+            capture_output=True, text=True, cwd=info["path"],
+        )
+        has_changes = bool(status.stdout.strip())
+        assert has_changes  # Should be dirty → not pruned
+        assert Path(info["path"]).exists()
+
+
+class TestEdgeCases:
+    """Test edge cases for robustness."""
+
+    def test_no_commits_repo(self, tmp_path):
+        """Worktree creation should fail gracefully on a repo with no commits."""
+        repo = tmp_path / "empty-repo"
+        repo.mkdir()
+        subprocess.run(["git", "init"], cwd=str(repo), capture_output=True)
+
+        info = _setup_worktree(str(repo))
+        assert info is None  # Should fail gracefully
+
+    def test_not_a_git_repo(self, tmp_path):
+        """Repo detection should return None for non-git directories."""
+        bare = tmp_path / "not-git"
+        bare.mkdir()
+        root = _git_repo_root(cwd=str(bare))
+        assert root is None
+
+    def test_worktrees_dir_already_exists(self, git_repo):
+        """Should work fine if .worktrees/ already exists."""
+        (git_repo / ".worktrees").mkdir(exist_ok=True)
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+        assert Path(info["path"]).exists()
+
+
+class TestCLIFlagLogic:
+    """Test the flag/config OR logic from main()."""
+
+    def test_worktree_flag_triggers(self):
+        """--worktree flag should trigger worktree creation."""
+        worktree = True
+        w = False
+        config_worktree = False
+        use_worktree = worktree or w or config_worktree
+        assert use_worktree
+
+    def test_w_flag_triggers(self):
+        """-w flag should trigger worktree creation."""
+        worktree = False
+        w = True
+        config_worktree = False
+        use_worktree = worktree or w or config_worktree
+        assert use_worktree
+
+    def test_config_triggers(self):
+        """worktree: true in config should trigger worktree creation."""
+        worktree = False
+        w = False
+        config_worktree = True
+        use_worktree = worktree or w or config_worktree
+        assert use_worktree
+
+    def test_none_set_no_trigger(self):
+        """No flags and no config should not trigger."""
+        worktree = False
+        w = False
+        config_worktree = False
+        use_worktree = worktree or w or config_worktree
+        assert not use_worktree
+
+
+class TestTerminalCWDIntegration:
+    """Test that TERMINAL_CWD is correctly set to the worktree path."""
+
+    def test_terminal_cwd_set(self, git_repo):
+        """After worktree setup, TERMINAL_CWD should point to the worktree."""
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # This is what main() does:
+        os.environ["TERMINAL_CWD"] = info["path"]
+        assert os.environ["TERMINAL_CWD"] == info["path"]
+        assert Path(os.environ["TERMINAL_CWD"]).exists()
+
+        # Clean up env
+        del os.environ["TERMINAL_CWD"]
+
+    def test_terminal_cwd_is_valid_git_repo(self, git_repo):
+        """The TERMINAL_CWD worktree should be a valid git working tree."""
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        result = subprocess.run(
+            ["git", "rev-parse", "--is-inside-work-tree"],
+            capture_output=True, text=True, cwd=info["path"],
+        )
+        assert result.stdout.strip() == "true"
+
+
+class TestSystemPromptInjection:
+    """Test that the agent gets worktree context in its system prompt."""
+
+    def test_prompt_note_format(self, git_repo):
+        """Verify the system prompt note contains all required info."""
+        info = _setup_worktree(str(git_repo))
+        assert info is not None
+
+        # This is what main() does:
+        wt_note = (
+            f"\n\n[System note: You are working in an isolated git worktree at "
+            f"{info['path']}. Your branch is `{info['branch']}`. "
+            f"Changes here do not affect the main working tree or other agents. "
+            f"Remember to commit and push your changes, and create a PR if appropriate. "
+            f"The original repo is at {info['repo_root']}.]"
+        )
+
+        assert info["path"] in wt_note
+        assert info["branch"] in wt_note
+        assert info["repo_root"] in wt_note
+        assert "isolated git worktree" in wt_note
+        assert "commit and push" in wt_note

website/docs/reference/cli-commands.md

@@ -22,6 +22,7 @@ These are commands you run from your shell.
 | `hermes chat --provider <name>` | Force a provider (`nous`, `openrouter`, `zai`, `kimi-coding`, `minimax`, `minimax-cn`) |
 | `hermes chat --toolsets "web,terminal"` / `-t` | Use specific toolsets |
 | `hermes chat --verbose` | Enable verbose/debug output |
+| `hermes --worktree` / `-w` | Start in an isolated git worktree (for parallel agents) |
 
 ### Provider & Model Management
 

website/docs/user-guide/cli.md

@@ -33,6 +33,10 @@ hermes --resume <session_id>  # Resume a specific session by ID (-r)
 
 # Verbose mode (debug output)
 hermes chat --verbose
+
+# Isolated git worktree (for running multiple agents in parallel)
+hermes -w                         # Interactive mode in worktree
+hermes -w -q "Fix issue #123"     # Single query in worktree
 ```
 
 ## Interface Layout

website/docs/user-guide/configuration.md

@@ -407,6 +407,26 @@ memory:
   user_char_limit: 1375     # ~500 tokens
 ```
 
+## Git Worktree Isolation
+
+Enable isolated git worktrees for running multiple agents in parallel on the same repo:
+
+```yaml
+worktree: true    # Always create a worktree (same as hermes -w)
+# worktree: false # Default — only when -w flag is passed
+```
+
+When enabled, each CLI session creates a fresh worktree under `.worktrees/` with its own branch. Agents can edit files, commit, push, and create PRs without interfering with each other. Clean worktrees are removed on exit; dirty ones are kept for manual recovery.
+
+You can also list gitignored files to copy into worktrees via `.worktreeinclude` in your repo root:
+
+```
+# .worktreeinclude
+.env
+.venv/
+node_modules/
+```
+
 ## Context Compression
 
 ```yaml