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

openspec/specs/git-repo/spec.md

@@ -6,7 +6,7 @@ Manage git repositories as bare repos on disk with metadata in database.
 ## Requirements
 ### Requirement: Repository Creation
 
-The system SHALL allow creating new bare git repositories.
+The system SHALL allow creating new bare git repositories with an optional SSH key association.
 
 #### Scenario: Create repository
 - GIVEN an authenticated user with a project
@@ -14,6 +14,25 @@ The system SHALL allow creating new bare git repositories.
 - THEN a bare repo is initialized on disk at `/data/repos/{user_id}/{project_id}/{repo_name}.git`
 - AND metadata is stored in the database
 
+#### Scenario: Create repository with SSH key
+- **GIVEN** an authenticated user with a project
+- **WHEN** they create a new repository with `ssh_key_id`
+- **THEN** a bare repo is initialized on disk
+- **AND** the SSH key association is stored in the database
+
+### Requirement: Repository SSH key assignment
+The system SHALL allow associating an SSH key with a GitRepository for clone operations and container git access.
+
+#### Scenario: Assign SSH key at repository creation
+- **GIVEN** an authenticated user creating a repository
+- **WHEN** they provide an `ssh_key_id`
+- **THEN** the repository is associated with that SSH key
+
+#### Scenario: Update repository SSH key
+- **GIVEN** an authenticated user with an existing repository
+- **WHEN** they call `PATCH /repositories/{id}/ssh-key` with a new `ssh_key_id`
+- **THEN** the repository's SSH key association is updated
+
 ### Requirement: Repository Cloning
 
 The system SHALL support cloning external repositories.