refactor: store workspaces as {workspace_id}/{repo_name} for natural git clone layout

Working copies were stored as /data/working-copies/{repo_id}/{workspace_name}/,
so git clone was forced into a user-named directory. That meant the container
mount basename was the workspace name (e.g. main) instead of the repo name.

- Generate the workspace UUID before cloning and clone into
  /data/working-copies/{workspace_id}/ so git creates {repo_name}/ naturally
- Set workspace.path to /data/working-copies/{workspace_id}/{repo_name}/
- Update _migrate_clone_into_workspace() to use the same layout
- _get_repository_mount_name() now prefers workspace.path basename and only
  falls back to remote URL / repo.name for legacy repo-only instances
- Update unit tests to assert workspace path basename is used for mounts

Quality gates:
- pytest tests/unit: 219 passed
- ruff: clean on changed files
- mypy: clean on changed files

apps/api/tests/unit/test_instance_service.py

@@ -64,6 +64,14 @@ class TestGetRepositoryMountName:
         repo.remote_url = "https://github.com/acme/headquarter/tree/main"
         assert _get_repository_mount_name(repo) == "headquarter"
 
+    def test_uses_workspace_path_basename_when_workspace_provided(self):
+        repo = MagicMock()
+        repo.name = "src"
+        repo.remote_url = "git@git.example.com:acme/headquarter.git"
+        workspace = MagicMock()
+        workspace.path = "/data/working-copies/uuid/headquarter"
+        assert _get_repository_mount_name(repo, workspace) == "headquarter"
+
     def test_falls_back_to_repo_name_when_remote_url_missing(self):
         repo = MagicMock()
         repo.name = "my-cool-repo"
@@ -78,13 +86,19 @@ class TestGetRepositoryMountName:
 
 
 @pytest.mark.unit
-async def test_prepare_manifest_instance_uses_repo_name_not_workspace_dir():
-    """WORKSPACE_NAME must be the repository name, not the workspace path basename."""
+async def test_prepare_manifest_instance_uses_workspace_path_basename():
+    """WORKSPACE_NAME must be the repo-named workspace directory, not workspace.name."""
     repo = MagicMock()
     repo.name = "src"
     repo.remote_url = "git@git.example.com:acme/headquarter.git"
     repo.path = "/data/repos/main"
 
+    workspace = MagicMock()
+    workspace.id = "workspace-uuid"
+    workspace.repo_id = "repo-uuid"
+    workspace.name = "main"
+    workspace.path = "/data/working-copies/workspace-uuid/headquarter"
+
     tool_type = MagicMock()
     tool_type.name = "pi-agent"
     tool_type.manifest_id = "manifest-uuid"
@@ -105,7 +119,7 @@ async def test_prepare_manifest_instance_uses_repo_name_not_workspace_dir():
     instance.tool_type_id = "tooltype-uuid"
     instance.port = 0
     instance.selected_config_profile_id = None
-    instance.workspace_id = None
+    instance.workspace_id = "workspace-uuid"
 
     session = AsyncMock()
 
@@ -116,6 +130,8 @@ async def test_prepare_manifest_instance_uses_repo_name_not_workspace_dir():
             return manifest_def
         if model.__name__ == "GitRepository":
             return repo
+        if model.__name__ == "Workspace":
+            return workspace
         return None
 
     session.get.side_effect = session_get
@@ -146,7 +162,7 @@ async def test_prepare_manifest_instance_uses_repo_name_not_workspace_dir():
             session=session,
             instance=instance,
             instance_dir="/tmp/instance",
-            repo_path="/data/repos/main",
+            repo_path="/data/working-copies/workspace-uuid/headquarter",
             env_vars={},
             extra_volumes=[],
             working_directory=None,
@@ -155,4 +171,4 @@ async def test_prepare_manifest_instance_uses_repo_name_not_workspace_dir():
         instance_service.subprocess.run = original_run
 
     assert "WORKSPACE_NAME: headquarter" in compose_content
-    assert "/data/repos/main:/home/user/headquarter" in compose_content
+    assert "/data/working-copies/workspace-uuid/headquarter:/home/user/headquarter" in compose_content