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/changes/git-repo-working-clones/tasks.md

@@ -1,19 +0,0 @@
-## 1. Backend - Repository Creation
-
-- [x] 1.1 Switch clone-based repository creation from mirror clones to normal working clones
-- [x] 1.2 Initialize blank repositories with a default branch name
-- [x] 1.3 Preserve remote preflight and clear error handling
-
-## 2. Backend - Git Sync Helpers
-
-- [x] 2.1 Update pull behavior to use the current tracked branch when available
-- [x] 2.2 Make branch helpers tolerate unborn HEAD in blank repos
-
-## 3. Tests
-
-- [x] 3.1 Add unit coverage for clone creation and blank repo initialization
-- [x] 3.2 Add coverage for pull behavior on working clones and blank repos
-
-## 4. Quality Gates
-
-- [x] 4.1 Run targeted API tests