## Why

Currently all tool instances bind-mount the host repository directory, giving containers live access to the working copy. Users need the ability to launch instances with an isolated fresh clone instead — useful for experimentation, clean-room development, or running tools that modify files without affecting the host copy. Additionally, containers need SSH key access to perform git operations (push/pull) inside the clone.

## What Changes

- **Repository-level SSH key assignment**: Each `GitRepository` can be associated with an SSH key (used for cloning and container git access). Configurable at creation time and editable later.
- **Clone mode for tool instances**: When creating a tool instance, users can choose between:
  - **Mount** (default): Bind-mount the host repository directory (current behavior)
  - **Clone**: Clone the repository into the instance directory with full history
- **Branch selection**: When clone mode is selected, users can specify a branch (defaults to `main`).
- **SSH key mounting**: The repository's SSH key is decrypted and mounted into the container's `~/.ssh/` directory, enabling git operations inside the container.
- **Dirty check on delete**: When deleting a clone-mode instance, check for uncommitted changes in the cloned repository. If changes exist, warn the user and require confirmation before deletion.
- **Frontend UI updates**: Sessions page gets a repository access mode selector (mount/clone), branch input, and SSH key selector when clone is chosen.
- **Backend API updates**: `POST /instances` accepts `clone_mode` and `branch`; new endpoint for updating repository SSH key.
- **Database migrations**: Add `ssh_key_id` to `git_repositories`, `clone_mode` and `branch` to `tool_instances`.

## Capabilities

### New Capabilities
- `repo-clone-mode`: Repository clone mode with host-side cloning, branch selection, and SSH key mounting for container git access.

### Modified Capabilities
- `git-repo`: Add `ssh_key_id` field and API for associating SSH keys with repositories.
- `tool-instances`: Extend instance creation to support `clone_mode` and `branch`, mount SSH keys at startup, and perform dirty check on deletion.

## Impact

- **Database**: Migrations for `git_repositories.ssh_key_id`, `tool_instances.clone_mode`, `tool_instances.branch`
- **Backend API**: `POST /instances` schema change, new `PATCH /repositories/{id}/ssh-key` endpoint, instance delete logic update
- **Frontend**: SessionsPage form additions, confirmation modal for dirty delete
- **Docker**: Dynamic SSH key volume injection via `_modify_compose_file`
- **Tool types**: Built-in tool images assumed to have git installed (code-server, jupyter do; opencode template already installs git)