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

docs/features/tool-types.md

@@ -62,6 +62,17 @@ services:
 - `{{TOOL_NAME}}` - Unique name for the container
 - `{{REPO_PATH}}` - Path to the repository
 
+#### Git Requirement for Clone Mode
+
+When users create instances in **clone mode** (fresh repository copy instead of bind mount), the container image must have `git` installed. This enables git operations (push, pull, branch) inside the container.
+
+**Built-in types with git:**
+- VS Code Server: Includes git
+- Jupyter Notebook: Includes git
+- OpenCode: Installs git during startup
+
+**Custom tool types:** Ensure your base image includes git (e.g., `apt-get install -y git` in Dockerfile).
+
 #### Validating Templates
 
 The system validates templates: