diff --git a/.pi-map.index.md b/.pi-map.index.md
index 71ffb76..692ed46 100644
--- a/.pi-map.index.md
+++ b/.pi-map.index.md
@@ -16,7 +16,7 @@ dir: .
 Trust boundary: index routes, map orients, source decides.
 
 ## role
-Infrastructure and deployment configuration for a self-hosted project management platform with OAuth2 authentication, providing Docker orchestration, environment templates, and development tooling.
+Infrastructure and deployment configuration for a self-hosted project management platform with multi-service Docker orchestration, SSO integration, and AI agent development guidelines.
 ## parent
 -
 ## children
diff --git a/.pi-map.md b/.pi-map.md
index 8d9b7f7..504822e 100644
--- a/.pi-map.md
+++ b/.pi-map.md
@@ -18,7 +18,7 @@ index: ./.pi-map.index.md
 Trust boundary: index routes, map orients, source decides.
 
 ## role
-Infrastructure and deployment configuration for a self-hosted project management platform with OAuth2 authentication, providing Docker orchestration, environment templates, and development tooling.
+Infrastructure and deployment configuration for a self-hosted project management platform with multi-service Docker orchestration, SSO integration, and AI agent development guidelines.
 ## files
 - .env.example | Provides a template of environment variables for configuring a Headquarter application with PostgreSQL, Redis, Authentik SSO, and Docker/Traefik deployment
 - .gitignore | Specifies files and directories for Git to ignore across a multi-language project with Python, Node, and custom tooling | dep: Git
@@ -31,7 +31,7 @@ Infrastructure and deployment configuration for a self-hosted project management
 - progress.md | Tracks completed and remaining tasks for a backend-frontend code refactoring project organized in 7 phases
 - swap-pane | Empty file with no functionality
 ## arch
-Containerized microservices architecture using Docker Compose with PostgreSQL/Redis data layer, Traefik reverse proxy for TLS/ingress, environment-driven configuration pattern, and Makefile-based lifecycle management across frontend/backend services.
+Containerized microservices architecture using Docker Compose with PostgreSQL/Redis data layer, Traefik reverse proxy for TLS/ingress, environment-driven configuration via dotenv, and OpenSpec-driven AI agent workflows.
 ## tags
 docker, redis, git, application, postgresql, compose, traefik, project
 ## symbols
diff --git a/apps/.pi-map.index.md b/apps/.pi-map.index.md
index fe888c5..3f1ff04 100644
--- a/apps/.pi-map.index.md
+++ b/apps/.pi-map.index.md
@@ -2,7 +2,7 @@
 dir: apps
 
 ## role
-Contains the main application entry points and executable modules for the project.
+Contains the deployable application entry points and executable configurations for the project.
 ## parent
 index: ./.pi-map.index.md
 map: ./.pi-map.md
diff --git a/apps/.pi-map.md b/apps/.pi-map.md
index 8532383..829e814 100644
--- a/apps/.pi-map.md
+++ b/apps/.pi-map.md
@@ -4,10 +4,10 @@ dir: apps
 index: apps/.pi-map.index.md
 
 ## role
-Contains the main application entry points and executable modules for the project.
+Contains the deployable application entry points and executable configurations for the project.
 ## files
 ## arch
-Modular application architecture with separate deployable units, likely following microservices or layered architecture patterns with domain-driven organization.
+Multi-app workspace structure with separate application boundaries, likely following micro-frontend or modular monolith patterns where each sub-directory represents an independent deployable unit.
 ## tags
 -
 ## symbols
diff --git a/apps/api/.pi-map.index.md b/apps/api/.pi-map.index.md
index e08a95e..89f89b1 100644
--- a/apps/api/.pi-map.index.md
+++ b/apps/api/.pi-map.index.md
@@ -2,7 +2,7 @@
 dir: apps/api
 
 ## role
-FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL database and async Alembic migrations.
+FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL persistence.
 ## parent
 index: apps/.pi-map.index.md
 map: apps/.pi-map.md
diff --git a/apps/api/.pi-map.md b/apps/api/.pi-map.md
index ff8b083..d758cb4 100644
--- a/apps/api/.pi-map.md
+++ b/apps/api/.pi-map.md
@@ -4,7 +4,7 @@ dir: apps/api
 index: apps/api/.pi-map.index.md
 
 ## role
-FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL database and async Alembic migrations.
+FastAPI backend API that manages projects, git repositories, and development tools via Docker instances with PostgreSQL persistence.
 ## 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 @@ FastAPI backend API that manages projects, git repositories, and development too
 - 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
-Self-hosted containerized service using multi-stage Docker builds, Cloudflare tunneling, uv package management, and startup dependency orchestration with shell-based health checks.
+Async Python/FastAPI service using multi-stage Docker builds, Alembic migrations, uv package management, and containerized deployment with Cloudflare tunneling support.
 ## tags
 docker, alembic, python, database, fastapi, postgresql, asyncpg, uvicorn
 ## symbols
diff --git a/apps/api/src/services/build/manifest_compiler.py b/apps/api/src/services/build/manifest_compiler.py
index 2fd25b1..a85d1d8 100644
--- a/apps/api/src/services/build/manifest_compiler.py
+++ b/apps/api/src/services/build/manifest_compiler.py
@@ -344,10 +344,10 @@ def compile_entrypoint(manifest: dict) -> str:
         lines.append("")
         lines.append("# Create /workspace compatibility symlink")
         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 [ "$(id -u)" = "0" ]; then')
+        lines.append('if [ "$(id -u)" = "0" ]; then')
         lines.append('    ln -sfn "$WORKSPACE_TARGET" /workspace')
+        lines.append('elif [ -n "$SUDO" ]; then')
+        lines.append('    sudo ln -sfn "$WORKSPACE_TARGET" /workspace')
         lines.append('else')
         lines.append('    ln -sfn "$WORKSPACE_TARGET" /workspace 2>/dev/null || true')
         lines.append('fi')
diff --git a/apps/api/tests/.pi-map.index.md b/apps/api/tests/.pi-map.index.md
index 77f726f..0f1f4e4 100644
--- a/apps/api/tests/.pi-map.index.md
+++ b/apps/api/tests/.pi-map.index.md
@@ -2,7 +2,7 @@
 dir: apps/api/tests
 
 ## role
-Provides shared test infrastructure and fixtures for the FastAPI API application.
+Provides shared test infrastructure and fixtures for the API test suite
 ## parent
 index: apps/api/.pi-map.index.md
 map: apps/api/.pi-map.md
diff --git a/apps/api/tests/.pi-map.md b/apps/api/tests/.pi-map.md
index fdff489..692437b 100644
--- a/apps/api/tests/.pi-map.md
+++ b/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 the FastAPI API application.
+Provides shared test infrastructure and fixtures for the API test suite
 ## 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 testing architecture with async SQLite database setup, authenticated HTTP client factories, and modular test data initialization.
+Pytest fixture-based testing architecture with async SQLite database setup, authenticated HTTP client factories, and modular test data seeding patterns
 ## tags
 call:app.dependency, call:create, overrides.get, call:override, fn, call:gen.asend, call:gen.aclose, user
 ## symbols
diff --git a/apps/api/tests/unit/.pi-map.index.md b/apps/api/tests/unit/.pi-map.index.md
index cd0a681..211f0d0 100644
--- a/apps/api/tests/unit/.pi-map.index.md
+++ b/apps/api/tests/unit/.pi-map.index.md
@@ -2,7 +2,7 @@
 dir: apps/api/tests/unit
 
 ## role
-Unit test suite for the API application covering configuration, database migrations, Docker operations, Git integration, file services, monitoring, notifications, and manifest compilation.
+Comprehensive unit test suite for the API application covering database migrations, configuration, git operations, Docker services, file handling, monitoring, and notification systems.
 ## parent
 index: apps/api/tests/.pi-map.index.md
 map: apps/api/tests/.pi-map.md
diff --git a/apps/api/tests/unit/.pi-map.md b/apps/api/tests/unit/.pi-map.md
index e0b2f20..dd46c5c 100644
--- a/apps/api/tests/unit/.pi-map.md
+++ b/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
-Unit test suite for the API application covering configuration, database migrations, Docker operations, Git integration, file services, monitoring, notifications, and manifest compilation.
+Comprehensive unit test suite for the API application covering database migrations, configuration, git operations, Docker services, file handling, monitoring, and notification systems.
 ## 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 @@ Unit test suite for the API application covering configuration, database migrati
 - 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 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_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_uses_root_then_sudo_for_workspace_symlink(self) → None, call:compile_entrypoint, call:entrypoint.find, 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 @@ Unit test suite for the API application covering configuration, database migrati
 - 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 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.
+Standard Python unittest/pytest structure with test files mirroring production modules, heavy use of mocking for external dependencies (Docker, subprocess, database), and isolated tests for individual service classes without integration requirements.
 ## tags
 test, url, call:notification, git, home, call:, merge, call:db
 ## symbols
diff --git a/apps/api/tests/unit/test_manifest_compiler.py b/apps/api/tests/unit/test_manifest_compiler.py
index 7584f34..e31044c 100644
--- a/apps/api/tests/unit/test_manifest_compiler.py
+++ b/apps/api/tests/unit/test_manifest_compiler.py
@@ -24,9 +24,16 @@ def test_compile_dockerfile_creates_config_dirs_for_user() -> None:
     assert "groupadd -g 1000 dev" in dockerfile
     assert "useradd -u 1000 -g 1000 -m -s /bin/bash dev" in dockerfile
     assert "mkdir -p /home/dev && chown -R dev:dev /home/dev" in dockerfile
-    assert "mkdir -p /home/dev/.config && chown -R dev:dev /home/dev/.config" in dockerfile
-    assert "mkdir -p /home/dev/.local/share && chown -R dev:dev /home/dev/.local/share" in dockerfile
-    assert "mkdir -p /home/dev/.cache && chown -R dev:dev /home/dev/.cache" in dockerfile
+    assert (
+        "mkdir -p /home/dev/.config && chown -R dev:dev /home/dev/.config" in dockerfile
+    )
+    assert (
+        "mkdir -p /home/dev/.local/share && chown -R dev:dev /home/dev/.local/share"
+        in dockerfile
+    )
+    assert (
+        "mkdir -p /home/dev/.cache && chown -R dev:dev /home/dev/.cache" in dockerfile
+    )
 
 
 @pytest.mark.unit
@@ -175,9 +182,7 @@ class TestCompileComposeHomeDirectory:
             "interface_type": "terminal",
             "home_directory": "/home/custom",
             "user": {"name": "dev", "uid": 1000, "gid": 1000},
-            "mounts": [
-                {"source_type": "repo", "target": "~/{{WORKSPACE_NAME}}"}
-            ],
+            "mounts": [{"source_type": "repo", "target": "~/{{WORKSPACE_NAME}}"}],
         }
         variables = {
             "IMAGE_TAG": "test:latest",
@@ -250,8 +255,8 @@ 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."""
+    def test_entrypoint_uses_root_then_sudo_for_workspace_symlink(self) -> None:
+        """/workspace is under /, so root takes precedence; non-root falls back to sudo."""
         manifest = {
             "base_image": "ubuntu:24.04",
             "interface_type": "terminal",
@@ -260,9 +265,12 @@ class TestCompileEntrypoint:
         }
         entrypoint = compile_entrypoint(manifest)
 
-        assert 'if [ -n "$SUDO" ]; then' in entrypoint
+        root_idx = entrypoint.find('if [ "$(id -u)" = "0" ]; then')
+        sudo_idx = entrypoint.find('elif [ -n "$SUDO" ]; then')
+        assert root_idx != -1
+        assert sudo_idx != -1
+        assert root_idx < sudo_idx
         assert 'sudo ln -sfn "$WORKSPACE_TARGET" /workspace' in entrypoint
-        assert 'elif [ "$(id -u)" = "0" ]; then' in entrypoint
 
     def test_entrypoint_fixes_mount_owners(self) -> None:
         manifest = {
@@ -279,4 +287,3 @@ class TestCompileEntrypoint:
 
         assert 'fix_owner "/home/custom/.config"' in entrypoint
         assert 'fix_owner "/opt/readonly"' not in entrypoint
-