feat: implement repository clone mode with SSH key support

- Add clone_mode and branch fields to tool_instances
- Add ssh_key_id to git_repositories for per-repo SSH key assignment
- Implement host-side git cloning with branch selection (default: main)
- Mount SSH keys into containers for git operations in clone mode
- Add dirty state check on clone-mode instance deletion with confirmation
- Update SessionsPage with mount/clone selector, branch input, SSH key display
- Add SSH key selector to repository creation form
- Add dirty delete confirmation modal with changed files list
- Update API schemas and endpoints for new fields
- Sync delta specs to main specs (git-repo, tool-instances, repo-clone-mode)
- Archive completed OpenSpec change: repo-clone-mode-with-ssh
- Document git requirement for custom tool types

Quality gates: Frontend typecheck and build passed
OpenSpec: repo-clone-mode-with-ssh archived with all tasks complete

apps/api/src/services/ssh_keys.py

@@ -0,0 +1,73 @@
+"""SSH key service utilities for preparing keys for container use."""
+
+import os
+from pathlib import Path
+
+from cryptography.fernet import Fernet
+
+from src.config import Settings
+
+
+def _get_fernet() -> Fernet:
+    """Generate a valid Fernet key from the session secret."""
+    import base64
+    import hashlib
+
+    settings = Settings()
+    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
+    key = base64.urlsafe_b64encode(key_bytes)
+    return Fernet(key)
+
+
+def prepare_ssh_key_files(instance_dir: str, ssh_key) -> str:
+    """Decrypt and write SSH key files to instance directory for container mounting.
+
+    Args:
+        instance_dir: Path to instance directory
+        ssh_key: SSHKey model instance with encrypted private key
+
+    Returns:
+        Path to the .ssh directory
+    """
+    ssh_dir = Path(instance_dir) / ".ssh"
+    ssh_dir.mkdir(parents=True, exist_ok=True)
+
+    # Decrypt private key
+    fernet = _get_fernet()
+    private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+
+    # Write private key with restricted permissions
+    private_key_path = ssh_dir / "id_ed25519"
+    private_key_path.write_text(private_key)
+    os.chmod(private_key_path, 0o600)
+
+    # Write public key
+    public_key_path = ssh_dir / "id_ed25519.pub"
+    public_key_path.write_text(ssh_key.public_key)
+    os.chmod(public_key_path, 0o644)
+
+    # Write SSH config
+    config_path = ssh_dir / "config"
+    config_content = """Host *
+    StrictHostKeyChecking no
+    UserKnownHostsFile /dev/null
+    IdentityFile ~/.ssh/id_ed25519
+    IdentitiesOnly yes
+"""
+    config_path.write_text(config_content)
+    os.chmod(config_path, 0o644)
+
+    return str(ssh_dir)
+
+
+def cleanup_ssh_key_files(instance_dir: str) -> None:
+    """Remove temporary SSH key files from instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+    """
+    ssh_dir = Path(instance_dir) / ".ssh"
+    if ssh_dir.exists():
+        for file_path in ssh_dir.iterdir():
+            file_path.unlink()
+        ssh_dir.rmdir()