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/models/git_repository.py

@@ -10,6 +10,7 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
+    from src.models.ssh_key import SSHKey
     from src.models.user import User
 
 
@@ -23,6 +24,10 @@ class GitRepository(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     is_mirror: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
     remote_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
     last_push: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
+    ssh_key_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("ssh_keys.id"), nullable=True
+    )
 
     project: Mapped["Project"] = relationship(back_populates="repositories")
     owner: Mapped["User"] = relationship()
+    ssh_key: Mapped["SSHKey | None"] = relationship()

apps/api/src/models/tool_instance.py

@@ -65,6 +65,12 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     probe_result: Mapped[dict | None] = mapped_column(
         JSON, nullable=True
     )
+    clone_mode: Mapped[str] = mapped_column(
+        String(20), nullable=False, default="mount"
+    )
+    branch: Mapped[str | None] = mapped_column(
+        String(255), nullable=True, default="main"
+    )
 
     tool_type: Mapped["ToolType"] = relationship()
     repository: Mapped["GitRepository"] = relationship()