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/src/services/tool/instance_service.py

@@ -20,6 +20,7 @@ from src.models import (
     SSHKey,
     ToolInstance,
     ToolType,
+    Workspace,
 )
 from src.schemas.tool import CreateInstanceRequest, StartInstanceRequest
 from src.services.git.clone import check_dirty_state, clone_repository
@@ -79,13 +80,21 @@ logger = logging.getLogger(__name__)
 _event_bus = InstanceEventBus()
 
 
-def _get_repository_mount_name(repo: GitRepository) -> str:
-    """Return the directory name a standard git clone would create.
+def _get_repository_mount_name(
+    repo: GitRepository,
+    workspace: "Workspace | None" = None,
+) -> str:
+    """Return the directory name the repository should appear under in the container.
 
-    Prefers the repository name parsed from the remote URL so the container
-    mount matches what users expect from ``git clone``. Falls back to the
-    user-provided repository name when no remote URL is available.
+    When a workspace exists, the on-disk layout is
+    ``/data/working-copies/{workspace_id}/{repo_name}/``, so the repo-named
+    directory is already available as the basename of ``workspace.path``. For
+    legacy repo-only instances we fall back to parsing the remote URL like a
+    standard ``git clone`` would, then to the user-provided repository name.
     """
+    if workspace is not None and workspace.path:
+        return os.path.basename(os.path.normpath(workspace.path))
+
     if repo.remote_url:
         base_url = extract_base_repo_url(repo.remote_url) or repo.remote_url
         name = base_url.rstrip("/").split("/")[-1]
@@ -907,10 +916,14 @@ async def prepare_manifest_instance(
 
     # Use the repository name for the workspace/repo mount target, not the
     # directory name of a workspace/clone path (which may be "main" or similar).
-    # Prefer the name parsed from the remote URL so it matches a standard clone.
+    # Prefer the actual on-disk workspace directory name when a workspace is
+    # mounted, otherwise fall back to parsing the remote URL like git clone.
     repo = await session.get(GitRepository, instance.repository_id)
+    workspace: Workspace | None = None
+    if instance.workspace_id:
+        workspace = await session.get(Workspace, instance.workspace_id)
     repo_name = (
-        _get_repository_mount_name(repo)
+        _get_repository_mount_name(repo, workspace)
         if repo
         else os.path.basename(os.path.normpath(repo_path))
     )
@@ -1075,7 +1088,7 @@ async def create_tool_instance(
         )
 
         home_dir = tool_type.home_directory or "/home/user"
-        mount_name = _get_repository_mount_name(repo)
+        mount_name = _get_repository_mount_name(repo, workspace)
         workspace_target = f"{home_dir}/{mount_name}"
 
         compose_content = f"""version: "3.8"\nservices:
@@ -1112,14 +1125,15 @@ async def create_tool_instance(
 
         # Manifest templates use WORKSPACE_PATH; REPO_PATH is retained as a
         # deprecated alias for backward compatibility with older templates.
+        mount_name = _get_repository_mount_name(repo, workspace)
         variables = {
             "IMAGE_TAG": image_tag,
             "INSTANCE_NAME": instance_name.lower(),
             "INSTANCE_DIR": instance_dir,
             "WORKSPACE_PATH": repo_path,
             "REPO_PATH": repo_path,
-            "REPO_NAME": _get_repository_mount_name(repo),
-            "WORKSPACE_NAME": _get_repository_mount_name(repo),
+            "REPO_NAME": mount_name,
+            "WORKSPACE_NAME": mount_name,
             "SSH_PATH": "",
             "TOOL_PORT": tool_port,
             "EXTRA_ENV": {},
@@ -1140,7 +1154,7 @@ async def create_tool_instance(
             "TOOL_PORT": tool_port,
             "USER_ID": str(user_id),
             "PROJECT_ID": str(project_id),
-            "WORKSPACE_NAME": _get_repository_mount_name(repo),
+            "WORKSPACE_NAME": _get_repository_mount_name(repo, workspace),
             "HOME_DIRECTORY": tool_type.home_directory or "/home/user",
         }
         compose_content = render_compose_template(tool_type.compose_template, variables)