feat: implement configurable tool container home directory

- Add ToolType.home_directory column with default /home/user
- Add Alembic migration to add column, set existing rows, and rewrite
  /workspace to /home/user/{{WORKSPACE_NAME}} in legacy templates
- Add merge migration fc8f1a20cbf6 to resolve Alembic multiple heads
- Update manifest compiler to honor manifest.home_directory for HOME,
  WORKDIR, /workspace symlink, and default repo mount target
- Update legacy dockerfile/compose instance generation to use
  tool_type.home_directory
- Thread resolved home_dir through config profile and git mount expansion
- Generate entrypoint permission fixer to chown home/mounts at startup
- Update base.dockerfile with sudo/passwordless sudo for permission fixer
- Add unit tests for manifest compiler, instance service, and migrations
- Add placeholder integration test for container lifecycle
- Update openspec/tasks/home-path-expansion.md task checkboxes
- Update project maps for modified files

Quality gates: py_compile, ruff, mypy, pytest tests/unit (205 passed),
pytest tests/integration (110 passed, 35 skipped). Alembic round-trip
and container lifecycle integration tests require Docker/PostgreSQL.

apps/api/tests/integration/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/api/tests/integration
 
 ## role
-Integration test suite for the API backend, covering authentication, workspaces, projects, notifications, configuration, and database models with real PostgreSQL and git repositories.
+Integration and unit test suite for the API backend, covering authentication, CRUD APIs, workspace operations, git integration, notifications, and database model validation against real PostgreSQL and mocked dependencies.
 ## parent
 index: apps/api/tests/.pi-map.index.md
 map: apps/api/tests/.pi-map.md
@@ -21,6 +21,7 @@ map: apps/api/tests/.pi-map.md
 - test_projects_api.py
 - test_seed.py
 - test_ssh_keys_api.py
+- test_tool_instance_lifecycle.py
 - test_tool_types_api.py
 - test_tool_types_api_extended.py
 - test_users_api.py