fix: use sudo/root to create /workspace symlink in manifest entrypoint

The previous commit moved the pi-agent repo mount from /workspace to
/home/user/{repo_name}. This exposed a permission bug: the Dockerfile
creates /workspace as a root-owned symlink in the image, and the
non-root entrypoint could not replace it because / is owned by root.

- Update compile_entrypoint to recreate /workspace via sudo when running
  as the container user, or directly when running as root
- Add unit test covering sudo/root symlink creation
- Update OpenSpec change docs with the additional root cause

Quality gates:
- pytest tests/unit: 208 passed
- ruff: clean on changed files
- mypy: clean on changed files
- alembic heads: single head

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

@@ -2,7 +2,7 @@
 dir: apps/api
 
 ## role
-Self-hosted FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL database.
+FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL database and async Alembic migrations.
 ## parent
 index: apps/.pi-map.index.md
 map: apps/.pi-map.md

apps/api/.pi-map.md

@@ -4,7 +4,7 @@ dir: apps/api
 index: apps/api/.pi-map.index.md
 
 ## role
-Self-hosted FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL database.
+FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL database and async Alembic migrations.
 ## files
 - .dockerignore | Specifies files and directories to exclude from Docker build context to reduce image size and avoid copying unnecessary files into containers. | dep: Docker
 - Dockerfile | Multi-stage Docker build for a Python application with Docker socket access, Cloudflare tunneling, and database dependency waiting | dep: python:3.11-slim, gcc, libpq-dev, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, pyproject.toml dependencies
@@ -14,7 +14,7 @@ Self-hosted FastAPI backend API that manages projects, git repositories, and dev
 - uv.lock | Lock file for the uv Python package manager that pins exact dependency versions and their artifact hashes for reproducible installations | dep: uv, Python 3.11+, aiosqlite, alembic, annotated-doc, annotated-types, anyio, ast-serialize, asyncpg, and many other PyPI packages
 - wait-for-db.sh | Wait for a PostgreSQL database to become available before executing a command, with configurable retry logic. | dep: nc (netcat), sh (POSIX shell), sleep
 ## arch
-Modern Python async architecture using FastAPI with SQLAlchemy/Alembic for database migrations, multi-stage Docker containerization with Docker socket access for container orchestration, Cloudflare tunneling for secure external access, and uv for fast dependency management.
+Self-hosted containerized service using multi-stage Docker builds, Cloudflare tunneling, uv package management, and startup dependency orchestration with shell-based health checks.
 ## tags
 docker, alembic, python, database, fastapi, postgresql, asyncpg, uvicorn
 ## symbols

apps/api/src/services/build/manifest_compiler.py

@@ -343,7 +343,14 @@ def compile_entrypoint(manifest: dict) -> str:
         lines.append('fix_owner "$WORKSPACE_TARGET"')
         lines.append("")
         lines.append("# Create /workspace compatibility symlink")
-        lines.append('ln -sfn "$WORKSPACE_TARGET" /workspace')
+        lines.append("# / is owned by root, so we need root or passwordless sudo.")
+        lines.append('if [ -n "$SUDO" ]; then')
+        lines.append('    sudo ln -sfn "$WORKSPACE_TARGET" /workspace')
+        lines.append('elif [ "$(id -u)" = "0" ]; then')
+        lines.append('    ln -sfn "$WORKSPACE_TARGET" /workspace')
+        lines.append('else')
+        lines.append('    ln -sfn "$WORKSPACE_TARGET" /workspace 2>/dev/null || true')
+        lines.append('fi')
         lines.append("")
         lines.append("# Fix ownership of declared mount targets (top-level only)")
         for mount in manifest.get("mounts", []):

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

@@ -2,7 +2,7 @@
 dir: apps/api/tests
 
 ## role
-Provides shared test infrastructure and fixtures for API integration testing with async database and authentication support.
+Provides shared test infrastructure and fixtures for the FastAPI API application.
 ## parent
 index: apps/api/.pi-map.index.md
 map: apps/api/.pi-map.md

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

@@ -4,11 +4,11 @@ dir: apps/api/tests
 index: apps/api/tests/.pi-map.index.md
 
 ## role
-Provides shared test infrastructure and fixtures for API integration testing with async database and authentication support.
+Provides shared test infrastructure and fixtures for the FastAPI API application.
 ## files
 - conftest.py | Provides shared pytest fixtures for testing a FastAPI application with async SQLite database, authenticated clients, and test data setup. | exp: func:test_client() → Generator[TestClient, None, None], call:create_async_engine, call:engine.begin, call:conn.run_sync, call:asyncio.run, call:init_db, call:async_sessionmaker, call:patch, call:TestClient, call:app.dependency_overrides.pop, call:engine.dispose, func:init_db(), call:engine.begin, call:conn.run_sync, func:override_get_db_session() → AsyncGenerator[AsyncSession, None], call:async_sessionmaker, func:db_session(test_client) → AsyncGenerator[AsyncSession, None], call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:gen.aclose, call:create_async_engine, call:engine.begin, call:conn.run_sync, call:async_sessionmaker, call:engine.dispose, func:authenticated_client(test_client) → Generator[TestClient, None, None], call:str, call:uuid.uuid4, call:Settings, call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:User, call:uuid.UUID, call:session.add, call:session.commit, call:gen.aclose, call:asyncio.run, call:create_test_user, call:create_session_cookie, call:test_client.cookies.set, func:create_test_user(), call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:User, call:uuid.UUID, call:session.add, call:session.commit, call:gen.aclose, func:test_project_and_repo(authenticated_client) → tuple[str, str], call:uuid.uuid4, call:Settings, call:authenticated_client.cookies.get, call:decode_session_cookie, call:uuid.UUID, call:asyncio.run, call:get_user_id, call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:Project, call:session.add, call:GitRepository, call:session.commit, call:gen.aclose, call:create_project_and_repo, call:str, raise:RuntimeError, func:get_user_id(), call:Settings, call:authenticated_client.cookies.get, call:decode_session_cookie, call:uuid.UUID, func:create_project_and_repo(), call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:Project, call:session.add, call:GitRepository, call:session.commit, call:gen.aclose, func:admin_client(test_client) → Generator[TestClient, None, None], call:str, call:uuid.uuid4, call:Settings, call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:User, call:uuid.UUID, call:session.add, call:session.commit, call:gen.aclose, call:asyncio.run, call:create_admin_user, call:create_session_cookie, call:test_client.cookies.set, func:create_admin_user(), call:app.dependency_overrides.get, call:override_fn, call:gen.asend, call:User, call:uuid.UUID, call:session.add, call:session.commit, call:gen.aclose | dep: asyncio, os, typing, unittest.mock, pytest, pytest_asyncio, fastapi.testclient, sqlalchemy.ext.asyncio, src.config, src.models.base, src.main, src.auth.dependencies, uuid, src.auth.session, src.models.user.user, src.models.project.project, src.models.project.git_repository, fastapi, sqlalchemy, aiosqlite, src.models, src.auth
 ## arch
-Pytest fixture-based architecture using dependency injection for async SQLite database sessions, JWT-authenticated HTTP clients, and modular test data setup across FastAPI test suites.
+Pytest fixture-based testing architecture with async SQLite database setup, authenticated HTTP client factories, and modular test data initialization.
 ## tags
 call:app.dependency, call:create, overrides.get, call:override, fn, call:gen.asend, call:gen.aclose, user
 ## symbols

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

@@ -2,12 +2,14 @@
 dir: apps/api/tests/unit
 
 ## role
-Contains unit tests for the API application's core services, utilities, and infrastructure components.
+Unit test suite for the API application covering configuration, database migrations, Docker operations, Git integration, file services, monitoring, notifications, and manifest compilation.
 ## parent
 index: apps/api/tests/.pi-map.index.md
 map: apps/api/tests/.pi-map.md
 ## children
--
+- apps/api/tests/unit/.ruff_cache
+  index: apps/api/tests/unit/.ruff_cache/.pi-map.index.md
+  map: apps/api/tests/unit/.ruff_cache/.pi-map.md
 ## files
 - __init__.py
 - test_alembic_migrations.py
@@ -40,5 +42,7 @@ map: apps/api/tests/unit/.pi-map.md
   read: __init__.py, test_alembic_migrations.py, test_config.py
 - change unit config
   read: test_config.py, test_config_profile_resolver.py
+- explore unit subdirectories
+  index: apps/api/tests/unit/.ruff_cache/.pi-map.index.md
 ## dirty
 -

apps/api/tests/unit/.pi-map.md

@@ -4,7 +4,7 @@ dir: apps/api/tests/unit
 index: apps/api/tests/unit/.pi-map.index.md
 
 ## role
-Contains unit tests for the API application's core services, utilities, and infrastructure components.
+Unit test suite for the API application covering configuration, database migrations, Docker operations, Git integration, file services, monitoring, notifications, and manifest compilation.
 ## files
 - __init__.py | Empty file with no functionality
 - test_alembic_migrations.py | Unit tests that verify Alembic database migrations are importable, have correct revision identifiers, and declare expected dependencies without requiring a live database. | exp: func:test_home_directory_migration_imports_and_rewrites() → None, call:Path, call:migration_path.exists, call:importlib.util.spec_from_file_location, call:importlib.util.module_from_spec, call:spec.loader.exec_module, call:callable, func:test_merge_migration_resolves_heads() → None, call:Path, call:migration_path.exists, call:importlib.util.spec_from_file_location, call:importlib.util.module_from_spec, call:spec.loader.exec_module, call:callable | dep: importlib.util, pathlib, pytest, importlib
@@ -21,7 +21,7 @@ Contains unit tests for the API application's core services, utilities, and infr
 - test_home_path_expansion.py | Unit tests for home directory path expansion (~ and $HOME) in container paths and manifest home directory resolution. | exp: class:TestExpandContainerPath, method:test_tilde_slash_expands(self) → None, call:expand_container_path, method:test_tilde_alone_expands(self) → None, call:expand_container_path, method:test_dollar_home_slash_expands(self) → None, call:expand_container_path, method:test_dollar_home_alone_expands(self) → None, call:expand_container_path, method:test_absolute_path_unchanged(self) → None, call:expand_container_path, method:test_relative_path_unchanged(self) → None, call:expand_container_path, method:test_tilde_in_middle_unchanged(self) → None, call:expand_container_path, method:test_dollar_home_in_middle_unchanged(self) → None, call:expand_container_path, method:test_root_home(self) → None, call:expand_container_path, class:TestGetManifestHomeDir, method:test_with_user_block(self) → None, call:get_manifest_home_dir, method:test_without_user_block(self) → None, call:get_manifest_home_dir, method:test_with_empty_user_name(self) → None, call:get_manifest_home_dir, method:test_with_none_user_name(self) → None, call:get_manifest_home_dir | dep: pytest, src.services.config.config_profile_resolver, src.services.build.manifest_compiler
 - test_instance_service.py | Unit tests for home directory expansion in docker-compose file modification via instance_service | exp: class:TestModifyComposeFile, method:test_extra_volumes_expand_home_dir(self, tmp_path), call:compose_path.write_text, call:modify_compose_file, call:str, call:compose_path.read_text, method:test_working_directory_expands_home_dir(self, tmp_path), call:compose_path.write_text, call:modify_compose_file, call:str, call:compose_path.read_text | dep: pytest, src.services.tool.instance_service
 - test_lifecycle_hooks.py | Unit tests for lifecycle hook helper functions that derive notification titles and determine whether events should trigger notifications. | exp: class:TestDeriveTitle, method:test_known_event_types(self) → None, call:_derive_title, method:test_unknown_event_type(self) → None, call:_derive_title, class:TestShouldNotify, method:test_error_events_are_notified(self) → None, call:_should_notify, method:test_health_changed_running_is_notified(self) → None, call:_should_notify, method:test_created_started_stopped_restarted_deleted_filtered(self) → None, call:_should_notify, method:test_health_changed_non_running_filtered(self) → None, call:_should_notify | dep: pytest, src.services.instance.lifecycle_hooks
-- test_manifest_compiler.py | Unit tests for a manifest compiler that generates Dockerfiles, docker-compose files, and entrypoint scripts from manifest configurations. | exp: class:TestGetManifestHomeDir, method:test_home_directory_in_manifest_wins(self) → None, call:get_manifest_home_dir, method:test_user_name_derives_home(self) → None, call:get_manifest_home_dir, method:test_root_fallback(self) → None, call:get_manifest_home_dir, method:test_empty_home_directory_falls_back(self) → None, call:get_manifest_home_dir, class:TestCompileDockerfileHomeDirectory, method:test_env_home_and_workdir_use_home_directory(self) → None, call:compile_dockerfile, method:test_workspace_symlink_created(self) → None, call:compile_dockerfile, method:test_runtime_working_dir_overrides_home_workdir(self) → None, call:compile_dockerfile, method:test_working_dir_expands_tilde(self) → None, call:compile_dockerfile, class:TestCompileComposeHomeDirectory, method:test_default_repo_mount_synthesized(self) → None, call:compile_compose, method:test_explicit_repo_mount_preserved(self) → None, call:compile_compose, method:test_workspace_name_substituted_in_mount_target(self) → None, call:compile_compose, method:test_working_dir_expands_home(self) → None, call:compile_compose, class:TestCompileEntrypoint, method:test_entrypoint_creates_home_and_workspace(self) → None, call:compile_entrypoint, method:test_entrypoint_fixes_mount_owners(self) → None, call:compile_entrypoint, func:test_compile_dockerfile_creates_config_dirs_for_user() → None, call:compile_dockerfile, func:test_compile_dockerfile_no_user_does_not_create_home() → None, call:compile_dockerfile, func:test_compile_dockerfile_uses_user_npm_prefix() → None, call:compile_dockerfile | dep: pytest, src.services.build.manifest_compiler
+- test_manifest_compiler.py | Unit tests for a manifest compiler that generates Dockerfiles, docker-compose files, and entrypoint scripts based on manifest configurations. | exp: class:TestGetManifestHomeDir, method:test_home_directory_in_manifest_wins(self) → None, call:get_manifest_home_dir, method:test_user_name_derives_home(self) → None, call:get_manifest_home_dir, method:test_root_fallback(self) → None, call:get_manifest_home_dir, method:test_empty_home_directory_falls_back(self) → None, call:get_manifest_home_dir, class:TestCompileDockerfileHomeDirectory, method:test_env_home_and_workdir_use_home_directory(self) → None, call:compile_dockerfile, method:test_workspace_symlink_created(self) → None, call:compile_dockerfile, method:test_runtime_working_dir_overrides_home_workdir(self) → None, call:compile_dockerfile, method:test_working_dir_expands_tilde(self) → None, call:compile_dockerfile, class:TestCompileComposeHomeDirectory, method:test_default_repo_mount_synthesized(self) → None, call:compile_compose, method:test_explicit_repo_mount_preserved(self) → None, call:compile_compose, method:test_workspace_name_substituted_in_mount_target(self) → None, call:compile_compose, method:test_working_dir_expands_home(self) → None, call:compile_compose, class:TestCompileEntrypoint, method:test_entrypoint_creates_home_and_workspace(self) → None, call:compile_entrypoint, method:test_entrypoint_uses_sudo_for_workspace_symlink(self) → None, call:compile_entrypoint, method:test_entrypoint_fixes_mount_owners(self) → None, call:compile_entrypoint, func:test_compile_dockerfile_creates_config_dirs_for_user() → None, call:compile_dockerfile, func:test_compile_dockerfile_no_user_does_not_create_home() → None, call:compile_dockerfile, func:test_compile_dockerfile_uses_user_npm_prefix() → None, call:compile_dockerfile | dep: pytest, src.services.build.manifest_compiler
 - test_migration_metadata.py | Tests Alembic database migration files for correct table definitions and revision chain metadata | exp: func:test_initial_migration_defines_all_core_tables() → None, call:Path(__file__).resolve, call:spec_from_file_location, call:module_from_spec, call:spec.loader.exec_module, func:test_refresh_tokens_migration_has_expected_revision_chain() → None, call:Path(__file__).resolve, call:spec_from_file_location, call:module_from_spec, call:spec.loader.exec_module | dep: pytest, importlib.util, pathlib, pathlib.Path
 - test_monitoring_models.py | Unit tests verifying creation, persistence, and querying of monitoring models (InstanceEvent and HealthCheck) with database migration compatibility. | exp: func:test_instance_event_creation(db_session) → None, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, call:ToolInstance, call:InstanceEvent, call:db_session.refresh, call:isinstance, func:test_health_check_creation(db_session) → None, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, call:ToolInstance, call:HealthCheck, call:db_session.refresh, call:isinstance, func:test_instance_event_query_by_instance(db_session) → None, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, call:ToolInstance, call:InstanceEvent, call:db_session.execute, call:select(InstanceEvent).where, call:result.scalar_one | dep: uuid, datetime, pytest, sqlalchemy, src.models.system.health_check, src.models.system.instance_event, src.models.tool.tool_instance, src.models.user.user
 - test_notification_service.py | Unit tests for NotificationService covering CRUD operations, filtering, sorting, and ownership isolation. | exp: func:notification_service() → NotificationService, call:NotificationService, func:user_a(db_session: AsyncSession) → User, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, func:user_b(db_session: AsyncSession) → User, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, func:test_create_notification(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:uuid.uuid4, func:test_list_notifications_orders_by_created_at_desc(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:datetime.now, call:timedelta, call:db_session.commit, call:db_session.refresh, call:notification_service.list_notifications, func:test_list_notifications_excludes_dismissed(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:notification_service.dismiss, call:notification_service.list_notifications, func:test_list_notifications_unread_only(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:notification_service.mark_read, call:notification_service.list_notifications, func:test_get_unread_count(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:range, call:notification_service.create_notification, call:notification_service.mark_read, call:notification_service.get_unread_count, func:test_mark_read_sets_read_at(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:notification_service.mark_read, func:test_mark_all_read_affects_all_unread(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:range, call:notification_service.create_notification, call:notification_service.mark_all_read, call:notification_service.get_unread_count, func:test_dismiss_sets_dismissed_at(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:notification_service.dismiss, call:db_session.execute, call:select(Notification).where, call:result.scalar_one, func:test_mark_read_wrong_owner_raises(db_session: AsyncSession, notification_service: NotificationService, user_a: User, user_b: User) → None, call:notification_service.create_notification, call:pytest.raises, call:notification_service.mark_read, func:test_dismiss_wrong_owner_raises(db_session: AsyncSession, notification_service: NotificationService, user_a: User, user_b: User) → None, call:notification_service.create_notification, call:pytest.raises, call:notification_service.dismiss, func:test_list_notifications_mute_categories(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:notification_service.list_notifications, func:test_get_unread_count_excludes_dismissed(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:notification_service.create_notification, call:notification_service.dismiss, call:notification_service.get_unread_count, func:test_dismiss_all_affects_all_non_dismissed(db_session: AsyncSession, notification_service: NotificationService, user_a: User) → None, call:range, call:notification_service.create_notification, call:notification_service.dismiss_all, call:notification_service.list_notifications, func:test_dismiss_all_affects_only_caller(db_session: AsyncSession, notification_service: NotificationService, user_a: User, user_b: User) → None, call:range, call:notification_service.create_notification, call:notification_service.dismiss_all, call:notification_service.list_notifications, func:test_mark_all_read_affects_only_caller(db_session: AsyncSession, notification_service: NotificationService, user_a: User, user_b: User) → None, call:range, call:notification_service.create_notification, call:notification_service.mark_all_read, call:notification_service.get_unread_count | dep: uuid, datetime, pytest, sqlalchemy, sqlalchemy.ext.asyncio, src.models.system.notification, src.models.user.user, src.services.shared.notification_service, NotificationService, Notification, User, AsyncSession
@@ -30,7 +30,7 @@ Contains unit tests for the API application's core services, utilities, and infr
 - test_readiness_probe.py | Unit tests for a Docker container readiness probe service that executes commands via docker exec with retry logic. | exp: class:TestExecuteProbe, class:TestIntegrationScenarios | dep: unittest.mock, src.services.shared.readiness_probe, subprocess
 - test_ssh_keys.py | Unit tests for SSH key preparation functionality including file creation, permissions, ownership, and error handling | exp: class:TestPrepareSshKeyFiles | dep: os, pathlib, unittest.mock, pytest, src.services.shared.ssh_keys
 ## arch
-Standard Python unittest/pytest pattern with heavy use of mocking for external dependencies (Docker, Git, subprocess, database) to test business logic in isolation without live services.
+Standard pytest-based unit testing with heavy use of mocking (subprocess, filesystem, database) to test components in isolation without external dependencies; tests are organized by service/feature with descriptive naming.
 ## tags
 test, url, call:notification, git, home, call:, merge, call:db
 ## symbols
@@ -47,5 +47,7 @@ test, url, call:notification, git, home, call:, merge, call:db
   read: __init__.py, test_alembic_migrations.py, test_config.py
 - change unit config
   read: test_config.py, test_config_profile_resolver.py
+- explore unit subdirectories
+  index: apps/api/tests/unit/.ruff_cache/.pi-map.index.md
 ## dirty
 -

apps/api/tests/unit/test_manifest_compiler.py

@@ -250,6 +250,20 @@ class TestCompileEntrypoint:
         assert 'ln -sfn "$WORKSPACE_TARGET" /workspace' in entrypoint
         assert 'WORKSPACE_NAME="${WORKSPACE_NAME:-workspace}"' in entrypoint
 
+    def test_entrypoint_uses_sudo_for_workspace_symlink(self) -> None:
+        """/workspace is under /, so the non-root entrypoint needs sudo to recreate it."""
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "interface_type": "terminal",
+            "home_directory": "/home/custom",
+            "user": {"name": "dev", "uid": 1000, "gid": 1000},
+        }
+        entrypoint = compile_entrypoint(manifest)
+
+        assert 'if [ -n "$SUDO" ]; then' in entrypoint
+        assert 'sudo ln -sfn "$WORKSPACE_TARGET" /workspace' in entrypoint
+        assert 'elif [ "$(id -u)" = "0" ]; then' in entrypoint
+
     def test_entrypoint_fixes_mount_owners(self) -> None:
         manifest = {
             "base_image": "ubuntu:24.04",