diff --git a/.pi-map.index.md b/.pi-map.index.md
index 655fa56..8661a76 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
-A self-hosted development platform that manages projects, git repositories, and development tools with OAuth2 authentication, containerized via Docker Compose.
+Root configuration and documentation package for "Headquarter," a self-hosted project management platform with Git repository features, containing deployment configs, development tooling, and UI rework tracking documents.
 ## parent
 -
 ## children
@@ -32,6 +32,15 @@ A self-hosted development platform that manages projects, git repositories, and
 - .pi
   index: .pi/.pi-map.index.md
   map: .pi/.pi-map.md
+- .pi-lens
+  index: .pi-lens/.pi-map.index.md
+  map: .pi-lens/.pi-map.md
+- .pytest_cache
+  index: .pytest_cache/.pi-map.index.md
+  map: .pytest_cache/.pi-map.md
+- .ruff_cache
+  index: .ruff_cache/.pi-map.index.md
+  map: .ruff_cache/.pi-map.md
 - .sisyphus
   index: .sisyphus/.pi-map.index.md
   map: .sisyphus/.pi-map.md
@@ -53,12 +62,12 @@ A self-hosted development platform that manages projects, git repositories, and
 - scripts
   index: scripts/.pi-map.index.md
   map: scripts/.pi-map.md
+- tests
+  index: tests/.pi-map.index.md
+  map: tests/.pi-map.md
 - tool-images
   index: tool-images/.pi-map.index.md
   map: tool-images/.pi-map.md
-- uploads
-  index: uploads/.pi-map.index.md
-  map: uploads/.pi-map.md
 ## files
 - .env.example
 - .gitignore
@@ -68,6 +77,7 @@ A self-hosted development platform that manages projects, git repositories, and
 - README.md
 - docker-compose.traefik.yml
 - docker-compose.yml
+- package-lock.json
 - progress.md
 - swap-pane
 - ui-audit-spacing-typography.md
diff --git a/.pi-map.md b/.pi-map.md
index a747817..909c12c 100644
--- a/.pi-map.md
+++ b/.pi-map.md
@@ -18,25 +18,26 @@ index: ./.pi-map.index.md
 Trust boundary: index routes, map orients, source decides.
 
 ## role
-A self-hosted development platform that manages projects, git repositories, and development tools with OAuth2 authentication, containerized via Docker Compose.
+Root configuration and documentation package for "Headquarter," a self-hosted project management platform with Git repository features, containing deployment configs, development tooling, and UI rework tracking documents.
 ## files
-- .env.example | Provides example environment variable configuration for a full-stack application with database, caching, authentication, and deployment settings
-- .gitignore | Specifies files and directories for Git to ignore across a project using Beads/Dolt, Python, Node, and various IDE/OS tooling. | dep: git, dolt, beads, python, node, npm, yarn, pnpm, pytest, mypy, ruff, coverage
-- AGENTS.md | Defines operational guidelines and workflows for AI agents collaborating on a software project governed by OpenSpec | dep: OpenSpec, superpowers (brainstorming, writing-plans, test-driven-development, systematic-debugging, verification-before-completion, using-git-worktrees, dispatching-parallel-agents), git
-- CHANGELOG.md | Documents version history and notable changes for a project management and Git repository application
-- Makefile | Provides standardized development commands for managing a Docker-based full-stack application with API, web frontend, database, and testing infrastructure | dep: docker compose, alembic, pytest, ruff, mypy, playwright, npm, postgres, redis
-- README.md | Documentation for a self-hosted development platform that manages projects, git repositories, and development tools with OAuth2 authentication | dep: FastAPI, SQLAlchemy, Pydantic, Alembic, python-jose, React, TypeScript, Vite, React Router, Docker, PostgreSQL, Traefik, Authentik
-- docker-compose.traefik.yml | Deploys a multi-service application (PostgreSQL, Redis, web frontend, API) behind an existing Traefik reverse proxy with TLS termination | dep: docker, docker-compose, traefik, postgres, redis, node/vite, python/fastapi
-- docker-compose.yml | Defines a multi-service Docker Compose stack for a web application with PostgreSQL, Redis, API backend, and web frontend services | dep: Docker, Docker Compose, PostgreSQL, Redis, Vite, asyncpg, Python/FastAPI (implied), Node.js (implied)
-- progress.md | Documents the progress and remaining tasks for a backend-frontend refactoring project involving modularization, code reorganization, and verification.
-- swap-pane | Provides a command to swap the position of two tmux panes within a window or between windows | dep: tmux, client, window, layout, cmd-find, cmd-parse, options
-- ui-audit-spacing-typography.md | A detailed audit report identifying critical CSS styling gaps, mobile layout failures, and design system inconsistencies in a web application's UI components and stylesheets. | dep: React/TSX components, CSS stylesheets (global.css, utilities.css, tokens.css, page-specific CSS), JSX/TSX files in apps/web/src/components and apps/web/src/pages
-- ui-rework-foundations-apply.md | Documents the implementation of Pass 1 (Foundations) of a web UI spacing/typography/visual-rhythm rework, including design token expansion, primitive CSS class additions, component refactors, and OpenSpec documentation. | dep: CSS design tokens, React/TSX components, OpenSpec documentation system, Git/SSH, npm build toolchain
-- ui-rework-pass2-apply.md | Documents the implementation of Pass 2 of a web UI spacing/typography rework, refactoring inline styles into token-based utility classes across multiple components. | dep: React/TSX components, CSS custom properties, OpenSpec documentation system, git workflow
+- .env.example | Provides a template of environment variables for configuring database, Redis, sessions, domains, Authentik OAuth, frontend, and Docker settings for the application. | dep: Postgres, Redis, Authentik, Vite, Docker Compose, Traefik
+- .gitignore | Specifies intentionally untracked files and directories to exclude from version control across multiple technologies and environments.
+- AGENTS.md | Defines rules, workflow conventions, and verification standards for AI agents operating on the project, using OpenSpec as the source of truth and Superpowers as the default workflow. | dep: OpenSpec, Superpowers, Git
+- CHANGELOG.md | Documents notable changes and version history for a project management application with Git repository features.
+- Makefile | Provides common development automation commands for a Dockerized full-stack application, including service lifecycle, testing, linting, migrations, and cleanup. | dep: docker compose, alembic, pytest, playwright, ruff, mypy, npm
+- README.md | Provides documentation and onboarding instructions for "Headquarter," a self-hosted platform for managing projects, git repositories, and development tools.
+- docker-compose.traefik.yml | Defines a Docker Compose deployment configuration for a multi-service application (PostgreSQL, Redis, web frontend, API) behind an existing Traefik reverse proxy with TLS termination. | dep: postgres:15-alpine, redis:7-alpine, traefik, docker.sock, authentik
+- docker-compose.yml | Defines a multi-container Docker Compose configuration for a full-stack application with PostgreSQL, Redis, an API service, and a web frontend. | dep: postgres:15-alpine, redis:7-alpine, apps/api, apps/web
+- package-lock.json | Locks dependency versions for the "headquarter" npm package.
+- progress.md | Tracks progress of a backend-frontend refactoring project across completed phases, pending tasks, and remaining work.
+- swap-pane | Empty package initialization file that marks a directory as a Python package.
+- ui-audit-spacing-typography.md | Audit report documenting spacing, typography, and visual rhythm issues in the web UI, including missing CSS classes, inconsistent units, incomplete design tokens, and recommendations for fixes.
+- ui-rework-foundations-apply.md | Documenting the implementation of Pass 1 (Foundations) of a web UI spacing/typography/visual-rhythm rework, summarizing changed files, commits, validation results, and next steps. | dep: tokens.css, global.css, utilities.css, ConfigProfileListSidebar.tsx, ConfigProfileEditorPanel.tsx, instance-list.tsx, openspec artifacts
+- ui-rework-pass2-apply.md | Implementation report documenting a UI component cleanup pass that refactored inline styles into CSS utility classes and design tokens.
 ## arch
-Full-stack containerized architecture with PostgreSQL database, Redis caching, separate API/backend and web frontend services, reverse-proxy ready (Traefik), using a Makefile-driven development workflow with AI agent collaboration via OpenSpec governance.
+Dockerized microservices architecture with PostgreSQL/Redis backend, separate API and web frontend services, Traefik reverse proxy option, npm-based frontend build, and Makefile-driven development workflow with phased UI refactoring tracked via markdown documents.
 ## tags
-docker, web, git, application, ui, rework, python, redis
+docker, ui, application, web, package, css, rework, redis
 ## symbols
 -
 ## workflows
diff --git a/apps/.pi-map.index.md b/apps/.pi-map.index.md
index fe888c5..31dccdd 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 main application entry points and executable components 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 f52628b..1639539 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 main application entry points and executable components for the project
 ## files
 ## arch
-Top-level directory for deployable application boundaries, typically organized by target platform or deployment variant (e.g., web, mobile, desktop, CLI).
+Modular application structure with separate deployable units, typically following framework-specific patterns (e.g., MVC, serverless handlers, or microservices)
 ## tags
 -
 ## symbols
diff --git a/apps/api/.pi-map.index.md b/apps/api/.pi-map.index.md
index b425eb4..9a6beba 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, development tools, and tool instances via Docker Compose
+Backend API server for the Headquarter platform, providing self-hosted project management, git repository orchestration, and development tool integration.
 ## parent
 index: apps/.pi-map.index.md
 map: apps/.pi-map.md
@@ -22,6 +22,12 @@ map: apps/.pi-map.md
 - apps/api/alembic
   index: apps/api/alembic/.pi-map.index.md
   map: apps/api/alembic/.pi-map.md
+- apps/api/app
+  index: apps/api/app/.pi-map.index.md
+  map: apps/api/app/.pi-map.md
+- apps/api/headquarter_api.egg-info
+  index: apps/api/headquarter_api.egg-info/.pi-map.index.md
+  map: apps/api/headquarter_api.egg-info/.pi-map.md
 - apps/api/src
   index: apps/api/src/.pi-map.index.md
   map: apps/api/src/.pi-map.md
diff --git a/apps/api/.pi-map.md b/apps/api/.pi-map.md
index 34cbd5d..7f57291 100644
--- a/apps/api/.pi-map.md
+++ b/apps/api/.pi-map.md
@@ -4,19 +4,19 @@ dir: apps/api
 index: apps/api/.pi-map.index.md
 
 ## role
-FastAPI backend API that manages projects, git repositories, development tools, and tool instances via Docker Compose
+Backend API server for the Headquarter platform, providing self-hosted project management, git repository orchestration, and development tool integration.
 ## files
-- .dockerignore | Specifies files and directories to exclude from Docker build context to reduce image size and avoid caching unnecessary files | dep: Docker
-- Dockerfile | Multi-stage Docker build for a Python web application with Docker socket access, database connectivity, and Cloudflare tunnel support | dep: python:3.11-slim, gcc, libpq-dev, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, pyproject.toml dependencies
-- README.md | README documentation for a self-hosted FastAPI backend API that manages projects, git repositories, development tools, and tool instances via Docker Compose | dep: FastAPI, SQLAlchemy, PostgreSQL, asyncpg, Alembic, Docker, Docker Compose, Authentik, uvicorn, pytest, ruff, mypy
-- alembic.ini | Configuration file for Alembic database migration tool, specifying script location, database connection URL, and logging settings | dep: alembic, sqlalchemy, asyncpg, postgresql
-- pyproject.toml | Defines Python project metadata, dependencies, and tool configurations for a FastAPI-based backend API called "headquarter-api" | dep: fastapi, uvicorn, sqlalchemy, asyncpg, alembic, pydantic, pydantic-settings, python-multipart, httpx, structlog, cryptography, pytest, pytest-asyncio, mypy, ruff, aiosqlite
-- uv.lock | Lock file generated by the uv Python package manager that pins exact dependency versions with cryptographic hashes for reproducible installations | dep: uv, python, pypi, aiosqlite, alembic, annotated-doc, annotated-types, anyio, ast-serialize, asyncpg, mako, sqlalchemy, typing-extensions, idna
-- wait-for-db.sh | Waits for a PostgreSQL database to become available by polling its TCP port before executing subsequent commands. | dep: nc (netcat), sh (POSIX shell), sleep
+- .dockerignore | Specifies files and directories to exclude from the Docker build context to optimize image build times and prevent sensitive or unnecessary files from being included.
+- Dockerfile | Multi-stage Dockerfile that builds and runs a Python application with Docker CLI access, cloudflared, and database readiness checks. | dep: python:3.11-slim, libpq5, git, openssh-client, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, netcat-openbsd
+- README.md | Provides comprehensive documentation for the Headquarter API, a self-hosted platform for managing projects, git repositories, and development tools. | dep: FastAPI, SQLAlchemy, PostgreSQL, asyncpg, Alembic, Docker, Authentik, Pydantic, Ruff, mypy, pytest
+- alembic.ini | Configuration file for Alembic database migration tool, defining database connection and logging settings. | dep: alembic, sqlalchemy, asyncpg, postgresql
+- pyproject.toml | Defines project metadata, dependencies, and tool configuration for the Headquarter platform API. | dep: fastapi, uvicorn, sqlalchemy, asyncpg, alembic, pydantic, pydantic-settings, httpx, structlog, cryptography, pytest, mypy, ruff
+- uv.lock | This file is a UV lockfile that pins exact versions, hashes, and metadata for all Python project dependencies to ensure reproducible environments. | dep: uv, aiosqlite, alembic, annotated-types, anyio, asyncpg, sqlalchemy, mako
+- wait-for-db.sh | Polls a PostgreSQL host/port until it is available or a retry limit is reached, then executes the passed command. | dep: nc, sleep
 ## arch
-Containerized Python microservice using FastAPI, SQLAlchemy with Alembic migrations, multi-stage Docker builds, and Docker Compose orchestration with external database dependency
+Python-based service using FastAPI/ASGI with Alembic for database migrations, multi-stage Docker containerization with cloudflared tunneling, UV for dependency management, and PostgreSQL as the primary datastore with explicit readiness-gated startup orchestration.
 ## tags
-docker, alembic, python, database, fastapi, sqlalchemy, asyncpg, uvicorn
+alembic, docker, sqlalchemy, asyncpg, dockerfile, database, postgresql, pydantic
 ## symbols
 -
 ## workflows
diff --git a/apps/api/src/.pi-map.index.md b/apps/api/src/.pi-map.index.md
index 3649c12..f4eceef 100644
--- a/apps/api/src/.pi-map.index.md
+++ b/apps/api/src/.pi-map.index.md
@@ -2,17 +2,23 @@
 dir: apps/api/src
 
 ## role
-Core FastAPI web application package that bootstraps and configures the Headquarter API service with database, authentication, logging, and modular routing infrastructure.
+Core FastAPI application package that initializes and configures the Headquarter API with database, authentication, logging, and middleware infrastructure.
 ## parent
 index: apps/api/.pi-map.index.md
 map: apps/api/.pi-map.md
 ## children
+- apps/api/src/.ruff_cache
+  index: apps/api/src/.ruff_cache/.pi-map.index.md
+  map: apps/api/src/.ruff_cache/.pi-map.md
 - apps/api/src/api
   index: apps/api/src/api/.pi-map.index.md
   map: apps/api/src/api/.pi-map.md
 - apps/api/src/auth
   index: apps/api/src/auth/.pi-map.index.md
   map: apps/api/src/auth/.pi-map.md
+- apps/api/src/headquarter_api.egg-info
+  index: apps/api/src/headquarter_api.egg-info/.pi-map.index.md
+  map: apps/api/src/headquarter_api.egg-info/.pi-map.md
 - apps/api/src/models
   index: apps/api/src/models/.pi-map.index.md
   map: apps/api/src/models/.pi-map.md
@@ -46,6 +52,6 @@ map: apps/api/src/.pi-map.md
 - change src config
   read: config.py, logging_config.py
 - explore src subdirectories
-  index: apps/api/src/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md, apps/api/src/models/.pi-map.index.md
+  index: apps/api/src/.ruff_cache/.pi-map.index.md, apps/api/src/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md
 ## dirty
 -
diff --git a/apps/api/src/.pi-map.md b/apps/api/src/.pi-map.md
index ae625ec..b026775 100644
--- a/apps/api/src/.pi-map.md
+++ b/apps/api/src/.pi-map.md
@@ -4,17 +4,17 @@ dir: apps/api/src
 index: apps/api/src/.pi-map.index.md
 
 ## role
-Core bootstrap and infrastructure package for the Headquarter API FastAPI application, handling configuration, database connectivity, logging, and application startup.
+Core FastAPI application package that initializes and configures the Headquarter API with database, authentication, logging, and middleware infrastructure.
 ## files
 - __init__.py | Marks the directory as a Python package for the Headquarter API.
-- config.py | Defines application configuration settings with environment-based overrides using Pydantic, including database URLs, domain/public URL resolution, Authentik OAuth integration, session/JWT settings, and cookie security policies. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
-- database.py | Configures an async SQLAlchemy database engine with session management and provides retry logic for database initialization via Alembic migrations. | exp: func:init_database(max_retries, retry_delay) → bool, call:range, call:engine.connect, call:test_conn.execute, call:text, call:test_conn.close, call:logger.info, call:asyncio.get_event_loop().run_in_executor, call:subprocess.run, call:os.path.dirname, call:os.path.abspath, call:logger.debug, call:logger.error, call:asyncio.sleep, call:str(exc).lower, call:logger.warning | dep: asyncio, logging, os, subprocess, sqlalchemy.ext.asyncio, sqlalchemy.pool, src.config, sqlalchemy
-- logging_config.py | Configures structured JSON logging with correlation IDs and HTTP request/exception middleware for a FastAPI application. | exp: class:CorrelationIdFilter, method:filter(self, record: logging.LogRecord) → bool, call:get_correlation_id, class:JSONFormatter, method:format(self, record: logging.LogRecord) → str, call:self.formatTime, call:record.getMessage, call:getattr, call:self.formatException, call:json.dumps, method:formatTime(self, record: logging.LogRecord, datefmt) → str, call:time.strftime, call:time.gmtime, class:RequestLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:time.time, call:logger.info, call:call_next, call:int, call:logger.error, call:type, call:traceback.format_exc, class:ExceptionLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:call_next, call:logger.critical, call:traceback.format_exc, func:configure_logging(level) → None, call:JSONFormatter, call:logging.StreamHandler, call:console_handler.setFormatter, call:console_handler.addFilter, call:CorrelationIdFilter, call:root_logger.setLevel, call:logging.getLogger("uvicorn").setLevel, call:logging.getLogger("uvicorn.access").setLevel, call:logging.getLogger("sqlalchemy.engine").setLevel, call:logger.info, call:logging.getLevelName | dep: json, logging, sys, time, traceback, collections.abc, fastapi, starlette.middleware.base, src.services.shared.correlation, starlette
-- main.py | Bootstraps a FastAPI application for "Headquarter API" with CORS, logging, validation error handling, database initialization, health monitoring, and registration of modular API routers. | exp: func:_sanitize_validation_errors(errors), call:error.get, call:str, call:ctx.items, call:isinstance, call:type, call:sanitized.append, func:validation_exception_handler(request: Request, exc: RequestValidationError), call:exc.errors, call:logger.warning, call:_sanitize_validation_errors, call:JSONResponse, func:on_startup(), call:logger.info, call:init_database, call:logger.error, call:sys.exit, call:_health_monitor.start, call:seed_builtin_tool_types, func:on_shutdown(), call:logger.info, call:_health_monitor.stop | dep: logging, os, fastapi, fastapi.exceptions, fastapi.middleware.cors, fastapi.responses, fastapi.staticfiles, src.api.config, src.api.project, src.api.system, src.api.tool, src.api.user, src.api.workspace, src.config, src.models, src.database, src.logging_config, src.seeds.builtin_tool_types, src.services.instance, src.services.shared, sys, src.api.*
+- config.py | Defines application configuration settings using pydantic-settings, including database connectivity, Authentik SSO, JWT, session, and domain-based URL resolution. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
+- database.py | Configures an async SQLAlchemy database engine/session and provides a retry-based initialization function that runs Alembic migrations via subprocess. | exp: func:init_database(max_retries, retry_delay) → bool, call:range, call:engine.connect, call:test_conn.execute, call:text, call:test_conn.close, call:logger.info, call:asyncio.get_event_loop().run_in_executor, call:subprocess.run, call:os.path.dirname, call:os.path.abspath, call:logger.debug, call:logger.error, call:asyncio.sleep, call:str(exc).lower, call:logger.warning | dep: asyncio, logging, os, subprocess, sqlalchemy.ext.asyncio, sqlalchemy.pool, src.config, sqlalchemy
+- logging_config.py | Configures structured JSON logging with correlation ID injection and provides ASGI middleware for logging HTTP requests, responses, and unhandled exceptions. | exp: class:CorrelationIdFilter, method:filter(self, record: logging.LogRecord) → bool, call:get_correlation_id, class:JSONFormatter, method:format(self, record: logging.LogRecord) → str, call:self.formatTime, call:record.getMessage, call:getattr, call:self.formatException, call:json.dumps, method:formatTime(self, record: logging.LogRecord, datefmt) → str, call:time.strftime, call:time.gmtime, class:RequestLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:time.time, call:logger.info, call:call_next, call:int, call:logger.error, call:type, call:traceback.format_exc, class:ExceptionLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:call_next, call:logger.critical, call:traceback.format_exc, func:configure_logging(level) → None, call:JSONFormatter, call:logging.StreamHandler, call:console_handler.setFormatter, call:console_handler.addFilter, call:CorrelationIdFilter, call:root_logger.setLevel, call:logging.getLogger("uvicorn").setLevel, call:logging.getLogger("uvicorn.access").setLevel, call:logging.getLogger("sqlalchemy.engine").setLevel, call:logger.info, call:logging.getLevelName | dep: json, logging, sys, time, traceback, collections.abc, fastapi, starlette.middleware.base, src.services.shared.correlation, starlette
+- main.py | Initializes and configures the FastAPI application, setting up middleware, routers, database connections, and lifecycle event handlers for the Headquarter API. | exp: func:_sanitize_validation_errors(errors), call:error.get, call:str, call:ctx.items, call:isinstance, call:type, call:sanitized.append, func:validation_exception_handler(request: Request, exc: RequestValidationError), call:exc.errors, call:logger.warning, call:_sanitize_validation_errors, call:JSONResponse, func:on_startup(), call:logger.info, call:init_database, call:logger.error, call:sys.exit, call:_health_monitor.start, call:seed_builtin_tool_types, func:on_shutdown(), call:logger.info, call:_health_monitor.stop | dep: logging, os, fastapi, fastapi.exceptions, fastapi.middleware.cors, fastapi.responses, fastapi.staticfiles, src.api.config, src.api.project, src.api.system, src.api.tool, src.api.user, src.api.workspace, src.config, src.models, src.database, src.logging_config, src.seeds.builtin_tool_types, src.services.instance, src.services.shared, sys, src.api, src.seeds, src.services
 ## arch
-Layered infrastructure pattern with Pydantic-based settings management, async SQLAlchemy with Alembic migrations, structured JSON logging with correlation ID tracking, and modular FastAPI router registration with middleware composition.
+Layered architecture using Pydantic-settings for configuration, async SQLAlchemy with Alembic migrations, structured JSON logging with correlation ID tracking, and FastAPI lifecycle management with dependency injection for cross-cutting concerns.
 ## tags
-src, database, logging, api, call:logger.info, fastapi, filter, call:logging.get
+src, logging, database, call:logger.info, api, middleware, filter, call:logging.get
 ## symbols
 - Settings
 - CorrelationIdFilter
@@ -30,6 +30,6 @@ src, database, logging, api, call:logger.info, fastapi, filter, call:logging.get
 - change src config
   read: config.py, logging_config.py
 - explore src subdirectories
-  index: apps/api/src/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md, apps/api/src/models/.pi-map.index.md
+  index: apps/api/src/.ruff_cache/.pi-map.index.md, apps/api/src/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md
 ## dirty
 -
diff --git a/apps/api/src/api/.pi-map.index.md b/apps/api/src/api/.pi-map.index.md
index a7dffb9..1be8cc4 100644
--- a/apps/api/src/api/.pi-map.index.md
+++ b/apps/api/src/api/.pi-map.index.md
@@ -2,11 +2,14 @@
 dir: apps/api/src/api
 
 ## role
-Defines reusable Pydantic validation utilities for API schema fields used across API endpoints.
+Defines the core API router package with reusable Pydantic validation utilities for container and filesystem-related API schemas.
 ## parent
 index: apps/api/src/.pi-map.index.md
 map: apps/api/src/.pi-map.md
 ## children
+- apps/api/src/api/.ruff_cache
+  index: apps/api/src/api/.ruff_cache/.pi-map.index.md
+  map: apps/api/src/api/.ruff_cache/.pi-map.md
 - apps/api/src/api/config
   index: apps/api/src/api/config/.pi-map.index.md
   map: apps/api/src/api/config/.pi-map.md
@@ -35,6 +38,6 @@ map: apps/api/src/api/.pi-map.md
 - change api behavior
   read: __init__.py, shared_validators.py
 - explore api subdirectories
-  index: apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md, apps/api/src/api/system/.pi-map.index.md
+  index: apps/api/src/api/.ruff_cache/.pi-map.index.md, apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md
 ## dirty
 -
diff --git a/apps/api/src/api/.pi-map.md b/apps/api/src/api/.pi-map.md
index 03f2d1e..8e6cc20 100644
--- a/apps/api/src/api/.pi-map.md
+++ b/apps/api/src/api/.pi-map.md
@@ -4,12 +4,12 @@ dir: apps/api/src/api
 index: apps/api/src/api/.pi-map.index.md
 
 ## role
-Defines reusable Pydantic validation utilities for API schema fields used across API endpoints.
+Defines the core API router package with reusable Pydantic validation utilities for container and filesystem-related API schemas.
 ## files
 - __init__.py | Marks the directory as a Python package for API routers.
-- shared_validators.py | Provides reusable Pydantic validation functions for API schema fields including mount paths, file uploads, environment variables, and volume mounts. | exp: func:validate_mount_path(v: str | None) → str | None, call:v.startswith, raise:ValueError, func:validate_files(v: dict | None, max_size_bytes) → dict | None, call:v.items, call:path.startswith, call:len, call:content.encode, raise:ValueError, func:validate_env_vars(v: dict | None) → dict | None, call:isinstance, raise:ValueError, func:validate_volumes(v: list | None) → list | None, call:isinstance, call:enumerate, raise:ValueError
+- shared_validators.py | Provides reusable Pydantic validator functions for validating mount paths, file contents, environment variables, and volume mounts in API schemas. | exp: func:validate_mount_path(v: str | None) → str | None, call:v.startswith, raise:ValueError, func:validate_files(v: dict | None, max_size_bytes) → dict | None, call:v.items, call:path.startswith, call:len, call:content.encode, raise:ValueError, func:validate_env_vars(v: dict | None) → dict | None, call:isinstance, raise:ValueError, func:validate_volumes(v: list | None) → list | None, call:isinstance, call:enumerate, raise:ValueError
 ## arch
-Utility module pattern with shared validation functions for common Docker/container resource types (mounts, volumes, files, environment variables).
+Modular package structure separating router organization from shared cross-cutting validation concerns using Pydantic validators.
 ## tags
 validate, raise:value, error, call:isinstance, mount, api, init, path
 ## symbols
@@ -25,6 +25,6 @@ validate, raise:value, error, call:isinstance, mount, api, init, path
 - change api behavior
   read: __init__.py, shared_validators.py
 - explore api subdirectories
-  index: apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md, apps/api/src/api/system/.pi-map.index.md
+  index: apps/api/src/api/.ruff_cache/.pi-map.index.md, apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md
 ## dirty
 -
diff --git a/apps/api/src/api/system/.pi-map.index.md b/apps/api/src/api/system/.pi-map.index.md
index c6f29bc..d6627c1 100644
--- a/apps/api/src/api/system/.pi-map.index.md
+++ b/apps/api/src/api/system/.pi-map.index.md
@@ -2,12 +2,14 @@
 dir: apps/api/src/api/system
 
 ## role
-Provides system-level infrastructure endpoints for monitoring, real-time communication, and instance management in the API service.
+Provides system-level API endpoints for monitoring, administration, and infrastructure operations including dashboards, health checks, event streaming, instance proxying, notifications, and terminal access.
 ## parent
 index: apps/api/src/api/.pi-map.index.md
 map: apps/api/src/api/.pi-map.md
 ## children
--
+- apps/api/src/api/system/.ruff_cache
+  index: apps/api/src/api/system/.ruff_cache/.pi-map.index.md
+  map: apps/api/src/api/system/.ruff_cache/.pi-map.md
 ## files
 - __init__.py
 - dashboard.py
@@ -22,5 +24,7 @@ map: apps/api/src/api/system/.pi-map.md
 ## workflows
 - change system behavior
   read: __init__.py, dashboard.py, events.py
+- explore system subdirectories
+  index: apps/api/src/api/system/.ruff_cache/.pi-map.index.md
 ## dirty
 -
diff --git a/apps/api/src/api/system/.pi-map.md b/apps/api/src/api/system/.pi-map.md
index 9cb02f9..2704c4b 100644
--- a/apps/api/src/api/system/.pi-map.md
+++ b/apps/api/src/api/system/.pi-map.md
@@ -4,19 +4,19 @@ dir: apps/api/src/api/system
 index: apps/api/src/api/system/.pi-map.index.md
 
 ## role
-Provides system-level infrastructure endpoints for monitoring, real-time communication, and instance management in the API service.
+Provides system-level API endpoints for monitoring, administration, and infrastructure operations including dashboards, health checks, event streaming, instance proxying, notifications, and terminal access.
 ## files
-- __init__.py | Aggregates and re-exports system API router modules for centralized access | dep: src.api.system.dashboard, src.api.system.events, src.api.system.health, src.api.system.instance_proxy, src.api.system.notifications, src.api.system.terminal
-- dashboard.py | Provides a FastAPI endpoint that returns a dashboard summary with aggregated counts and recent activity for the authenticated user. | exp: func:get_dashboard_summary(user_id, session) → dict, call:session.execute, call:select(func.count()).select_from(Project).where, call:func.count, call:projects_result.scalar, call:select(func.count()).select_from(GitRepository).where, call:repos_result.scalar, call:select(func.count()).select_from(SSHKey).where, call:ssh_keys_result.scalar, call:select(Project) .where(Project.owner_id == user_id) .order_by(Project.created_at.desc()) .limit, call:Project.created_at.desc, call:recent_projects.scalars().all | dep: uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.models.project
-- events.py | Implements an SSE streaming endpoint that delivers instance events to authenticated users with per-user connection limiting and automatic heartbeat pings. | exp: func:events_stream(request: Request, user_id) → StreamingResponse, call:_connection_counts.get, call:InstanceEventBus, call:asyncio.Queue, call:queue.put_nowait, call:contextlib.suppress, call:queue.get_nowait, call:event_bus.subscribe, call:asyncio.wait_for, call:queue.get, call:json.dumps, call:unsubscribe, call:max, call:_connection_counts.pop, call:StreamingResponse, call:event_generator, raise:HTTPException, func:event_generator() → AsyncGenerator[str, None], call:InstanceEventBus, call:asyncio.Queue, call:queue.put_nowait, call:contextlib.suppress, call:queue.get_nowait, call:event_bus.subscribe, call:asyncio.wait_for, call:queue.get, call:json.dumps, call:unsubscribe, call:max, call:_connection_counts.get, call:_connection_counts.pop, func:on_event(payload: InstanceEventPayload) → None, call:queue.put_nowait, call:contextlib.suppress, call:queue.get_nowait | dep: asyncio, contextlib, json, uuid, collections.abc, fastapi, fastapi.responses, src.auth.dependencies, src.services.instance.event_bus
+- __init__.py | Aggregates and exports system API routers for a modular web application framework. | dep: src.api.system.dashboard, src.api.system.events, src.api.system.health, src.api.system.instance_proxy, src.api.system.notifications, src.api.system.terminal
+- dashboard.py | Provides a FastAPI endpoint that returns a dashboard summary with counts of projects, repositories, SSH keys, and recent activity for the authenticated user. | exp: func:get_dashboard_summary(user_id, session) → dict, call:session.execute, call:select(func.count()).select_from(Project).where, call:func.count, call:projects_result.scalar, call:select(func.count()).select_from(GitRepository).where, call:repos_result.scalar, call:select(func.count()).select_from(SSHKey).where, call:ssh_keys_result.scalar, call:select(Project) .where(Project.owner_id == user_id) .order_by(Project.created_at.desc()) .limit, call:Project.created_at.desc, call:recent_projects.scalars().all | dep: uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.models.project
+- events.py | Implements an SSE streaming endpoint that delivers instance events to authenticated users with per-user connection limits and heartbeat pings. | dep: asyncio, contextlib, json, uuid, collections.abc, fastapi, src.auth.dependencies, src.services.instance.event_bus
 - health.py | Provides FastAPI health check endpoints that monitor system health including database connectivity/response time and disk usage, returning structured health status responses. | exp: func:health_check() → dict[str, Any], call:HealthChecks, call:time_module.perf_counter, call:SessionLocal, call:session.execute, call:text, call:DatabaseHealth, call:round, call:shutil.disk_usage, call:DiskHealth, call:HealthResponse( status=overall_status, timestamp=datetime.now(timezone.utc).isoformat().replace("+00:00", "Z"), version="0.1.0", checks=checks, uptime_seconds=round(time.time() - _start_time, 2), ).model_dump, call:datetime.now(timezone.utc).isoformat().replace, call:time.time, func:health_check_db() → dict[str, Any], call:time_module.perf_counter, call:SessionLocal, call:session.execute, call:text, call:DatabaseHealthResponse( status="healthy", response_time_ms=round(db_time, 2), ).model_dump, call:round, call:DatabaseHealthResponse( status="unhealthy", response_time_ms=0.0, ).model_dump | dep: time, datetime, typing, fastapi, sqlalchemy, src.database, src.schemas.system, shutil
-- instance_proxy.py | HTTP request proxy router that forwards requests from authenticated users to their running containerized tool instances. | exp: func:_proxy_request(request: Request, instance_id: uuid.UUID, path: str, user_id: uuid.UUID, session: AsyncSession) → Response, call:session.get, call:str, call:request.headers.items, call:key.lower, call:httpx.AsyncClient, call:request.body, call:client.request, call:logger.error, call:dict, call:response_headers.pop, call:Response, raise:HTTPException, func:proxy_to_instance(request: Request, instance_id: uuid.UUID, path, user_id, session) → Response, call:_proxy_request | dep: logging, uuid, httpx, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models
-- notifications.py | Defines FastAPI REST endpoints for managing user notifications (list, unread count, mark read, dismiss, clear all) with support for muted categories. | exp: class:NotificationItem, class:NotificationListResponse, class:UnreadCountResponse, class:MarkAllReadResponse, class:ClearAllResponse, func:_get_mute_categories(session: AsyncSession, user_id: uuid.UUID) → list[str], call:session.execute, call:select(UserConfig).where, call:result.scalar_one_or_none, call:config.config.get, call:isinstance, func:list_notifications(limit, offset, unread_only, user, session) → NotificationListResponse, call:_get_mute_categories, call:notification_service.list_notifications, call:NotificationListResponse, call:NotificationItem.model_validate, func:get_unread_count(user, session) → UnreadCountResponse, call:notification_service.get_unread_count, call:UnreadCountResponse, func:mark_notification_read(notification_id: uuid.UUID, user, session) → NotificationItem, call:notification_service.mark_read, call:NotificationItem.model_validate, raise:HTTPException, func:mark_all_read(user, session) → MarkAllReadResponse, call:notification_service.mark_all_read, call:MarkAllReadResponse, func:clear_all_notifications(user, session) → ClearAllResponse, call:notification_service.dismiss_all, call:ClearAllResponse, func:dismiss_notification(notification_id: uuid.UUID, user, session) → None, call:notification_service.dismiss, raise:HTTPException | dep: uuid, datetime, fastapi, pydantic, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models.user, src.models, src.services.shared.notification_service, sqlalchemy, src.models.UserConfig
-- terminal.py | Provides WebSocket endpoints for browser-based terminal access to running tool instances, handling session lifecycle, authentication, input/output streaming, and terminal resize/reset operations. | exp: class:SessionRef, method:__init__(self, session, slot_session_id), func:terminal_websocket_default(websocket: WebSocket, instance_id: str, db_session) → None, call:_handle_terminal_websocket, func:terminal_websocket_specific(websocket: WebSocket, instance_id: str, session_id: str, db_session) → None, call:_handle_terminal_websocket, func:_resolve_container_user(db_session: AsyncSession, instance: ToolInstance) → str | None, call:db_session.get, call:dict, call:resolve_base, call:deep_merge, call:get_manifest_container_user, func:_handle_terminal_websocket(websocket: WebSocket, instance_id: str, target_session_id: str | None, db_session: AsyncSession) → None, call:logger.debug, call:websocket.accept, call:uuid.UUID, call:logger.error, call:websocket.close, call:_get_user_from_websocket, call:logger.warning, call:db_session.get, call:get_container_status, call:_resolve_container_user, call:terminal_manager.get_or_create_session, call:terminal_manager.get_session, call:logger.info, call:terminal_manager.create_session, call:terminal_manager._find_key_by_internal_id, call:terminal_manager.attach_websocket, call:websocket.send_json, call:SessionRef, call:asyncio.create_task, call:_write_loop, call:_heartbeat_loop, call:asyncio.wait, call:len, call:task.cancel, call:str, call:suppress, call:terminal_manager.detach_websocket, func:_write_loop(session_ref: SessionRef, websocket, instance_id: str) → None, call:session.is_alive, call:asyncio.sleep, call:websocket.receive, call:session.write_input, call:text.startswith, call:json.loads, call:ctrl.get, call:logger.debug, call:session.resize, call:session.acknowledge_data, call:websocket.send_json, call:terminal_manager.reset_session, call:terminal_manager.attach_websocket, call:text.encode, func:_heartbeat_loop(websocket: WebSocket) → None, call:asyncio.sleep, call:websocket.send_json, func:_get_terminal_instance(instance_id: uuid.UUID, user_id: uuid.UUID, db_session: AsyncSession) → ToolInstance, call:db_session.get, raise:HTTPException, func:list_terminal_sessions(instance_id: uuid.UUID, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.execute, call:select(TerminalSessionModel) .where(TerminalSessionModel.instance_id == instance_id) .where(TerminalSessionModel.status != "closed") .order_by, call:TerminalSessionModel.created_at.asc, call:result.scalars().all, call:terminal_manager.get_session, call:str, call:sessions.append, call:live_session.has_websockets, call:row.created_at.isoformat, call:row.last_activity_at.isoformat, func:create_terminal_session(instance_id: uuid.UUID, data: dict, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.get, call:data.get, call:_resolve_container_user, call:terminal_manager.create_session, raise:HTTPException, func:close_terminal_session(instance_id: uuid.UUID, session_id: str, user_id, db_session) → dict, call:_get_terminal_instance, call:terminal_manager._find_key_by_internal_id, call:str, call:terminal_manager.get_session, call:terminal_manager.close_session, raise:HTTPException, func:reset_specific_terminal_session(instance_id: uuid.UUID, session_id: str, user_id, db_session) → dict, call:_get_terminal_instance, call:terminal_manager._find_key_by_internal_id, call:str, call:terminal_manager.get_session, call:db_session.get, call:_resolve_container_user, call:terminal_manager.reset_session, raise:HTTPException, func:rename_terminal_session(instance_id: uuid.UUID, session_id: str, data: dict, user_id, db_session) → dict, call:_get_terminal_instance, call:data.get, call:isinstance, call:terminal_manager.get_session, call:str, call:db_session.get, call:uuid.UUID, call:db_session.commit, raise:HTTPException, func:reset_terminal_session(instance_id: uuid.UUID, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.get, call:_resolve_container_user, call:terminal_manager.reset_session, call:logger.info, call:str, call:logger.error, raise:HTTPException, func:_get_user_from_websocket(websocket: WebSocket, db_session: AsyncSession) → uuid.UUID | None, call:websocket.cookies.get, call:Settings, call:decode_session_cookie, call:uuid.UUID, call:str | dep: asyncio, json, logging, uuid, contextlib, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, starlette.websockets, src.auth.dependencies, src.models, src.services.build.manifest_compiler, src.services.terminal.terminal_manager, src.services.docker, src.auth.session, src.config, starlette
+- instance_proxy.py | Proxies HTTP requests from authenticated users to running containerized tool instances after verifying ownership and instance status. | exp: func:_proxy_request(request: Request, instance_id: uuid.UUID, path: str, user_id: uuid.UUID, session: AsyncSession) → Response, call:session.get, call:str, call:request.headers.items, call:key.lower, call:httpx.AsyncClient, call:request.body, call:client.request, call:logger.error, call:dict, call:response_headers.pop, call:Response, raise:HTTPException, func:proxy_to_instance(request: Request, instance_id: uuid.UUID, path, user_id, session) → Response, call:_proxy_request | dep: logging, uuid, httpx, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models
+- notifications.py | Defines FastAPI REST endpoints for user notification management including listing, marking as read, dismissing, and retrieving unread counts with support for muted categories. | exp: class:NotificationItem, class:NotificationListResponse, class:UnreadCountResponse, class:MarkAllReadResponse, class:ClearAllResponse, func:_get_mute_categories(session: AsyncSession, user_id: uuid.UUID) → list[str], call:session.execute, call:select(UserConfig).where, call:result.scalar_one_or_none, call:config.config.get, call:isinstance, func:list_notifications(limit, offset, unread_only, user, session) → NotificationListResponse, call:_get_mute_categories, call:notification_service.list_notifications, call:NotificationListResponse, call:NotificationItem.model_validate, func:get_unread_count(user, session) → UnreadCountResponse, call:notification_service.get_unread_count, call:UnreadCountResponse, func:mark_notification_read(notification_id: uuid.UUID, user, session) → NotificationItem, call:notification_service.mark_read, call:NotificationItem.model_validate, raise:HTTPException, func:mark_all_read(user, session) → MarkAllReadResponse, call:notification_service.mark_all_read, call:MarkAllReadResponse, func:clear_all_notifications(user, session) → ClearAllResponse, call:notification_service.dismiss_all, call:ClearAllResponse, func:dismiss_notification(notification_id: uuid.UUID, user, session) → None, call:notification_service.dismiss, raise:HTTPException | dep: uuid, datetime, fastapi, pydantic, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models.user, src.models, src.services.shared.notification_service, sqlalchemy
+- terminal.py | Provides WebSocket endpoints for browser-based terminal access to running Docker container tool instances, handling authentication, session management, input/output streaming, and terminal resize/reset operations. | exp: class:SessionRef, method:__init__(self, session, slot_session_id), func:terminal_websocket_default(websocket: WebSocket, instance_id: str, db_session) → None, call:_handle_terminal_websocket, func:terminal_websocket_specific(websocket: WebSocket, instance_id: str, session_id: str, db_session) → None, call:_handle_terminal_websocket, func:_resolve_container_user(db_session: AsyncSession, instance: ToolInstance) → str | None, call:db_session.get, call:dict, call:resolve_base, call:deep_merge, call:get_manifest_container_user, func:_handle_terminal_websocket(websocket: WebSocket, instance_id: str, target_session_id: str | None, db_session: AsyncSession) → None, call:logger.debug, call:websocket.accept, call:uuid.UUID, call:logger.error, call:websocket.close, call:_get_user_from_websocket, call:logger.warning, call:db_session.get, call:get_container_status, call:_resolve_container_user, call:terminal_manager.get_or_create_session, call:terminal_manager.get_session, call:logger.info, call:terminal_manager.create_session, call:terminal_manager._find_key_by_internal_id, call:terminal_manager.attach_websocket, call:websocket.send_json, call:SessionRef, call:asyncio.create_task, call:_write_loop, call:_heartbeat_loop, call:asyncio.wait, call:len, call:task.cancel, call:str, call:suppress, call:terminal_manager.detach_websocket, func:_write_loop(session_ref: SessionRef, websocket, instance_id: str) → None, call:session.is_alive, call:asyncio.sleep, call:websocket.receive, call:session.write_input, call:text.startswith, call:json.loads, call:ctrl.get, call:logger.debug, call:session.resize, call:session.acknowledge_data, call:websocket.send_json, call:terminal_manager.reset_session, call:terminal_manager.attach_websocket, call:text.encode, func:_heartbeat_loop(websocket: WebSocket) → None, call:asyncio.sleep, call:websocket.send_json, func:_get_terminal_instance(instance_id: uuid.UUID, user_id: uuid.UUID, db_session: AsyncSession) → ToolInstance, call:db_session.get, raise:HTTPException, func:list_terminal_sessions(instance_id: uuid.UUID, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.execute, call:select(TerminalSessionModel) .where(TerminalSessionModel.instance_id == instance_id) .where(TerminalSessionModel.status != "closed") .order_by, call:TerminalSessionModel.created_at.asc, call:result.scalars().all, call:terminal_manager.get_session, call:str, call:sessions.append, call:live_session.has_websockets, call:row.created_at.isoformat, call:row.last_activity_at.isoformat, func:create_terminal_session(instance_id: uuid.UUID, data: dict, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.get, call:data.get, call:_resolve_container_user, call:terminal_manager.create_session, raise:HTTPException, func:close_terminal_session(instance_id: uuid.UUID, session_id: str, user_id, db_session) → dict, call:_get_terminal_instance, call:terminal_manager._find_key_by_internal_id, call:str, call:terminal_manager.get_session, call:terminal_manager.close_session, raise:HTTPException, func:reset_specific_terminal_session(instance_id: uuid.UUID, session_id: str, user_id, db_session) → dict, call:_get_terminal_instance, call:terminal_manager._find_key_by_internal_id, call:str, call:terminal_manager.get_session, call:db_session.get, call:_resolve_container_user, call:terminal_manager.reset_session, raise:HTTPException, func:rename_terminal_session(instance_id: uuid.UUID, session_id: str, data: dict, user_id, db_session) → dict, call:_get_terminal_instance, call:data.get, call:isinstance, call:terminal_manager.get_session, call:str, call:db_session.get, call:uuid.UUID, call:db_session.commit, raise:HTTPException, func:reset_terminal_session(instance_id: uuid.UUID, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.get, call:_resolve_container_user, call:terminal_manager.reset_session, call:logger.info, call:str, call:logger.error, raise:HTTPException, func:_get_user_from_websocket(websocket: WebSocket, db_session: AsyncSession) → uuid.UUID | None, call:websocket.cookies.get, call:Settings, call:decode_session_cookie, call:uuid.UUID, call:str | dep: asyncio, json, logging, uuid, contextlib, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, starlette.websockets, src.auth.dependencies, src.models, src.services.build.manifest_compiler, src.services.terminal.terminal_manager, src.services.docker, src.auth.session, src.config, starlette
 ## arch
-Modular FastAPI router composition with separate modules for distinct protocols (REST/SSE/WebSocket/proxy), each handling authentication, connection lifecycle management, and resource-specific business logic.
+Modular FastAPI router pattern with per-feature separation, combining standard REST endpoints, SSE streaming, and WebSocket connections, all with unified authentication and user-scoped access control.
 ## tags
-terminal, call:, session, call:terminal, src, get, response, websocket
+terminal, session, call:terminal, call:, src, get, response, instance
 ## symbols
 - NotificationItem
 - NotificationListResponse
@@ -25,9 +25,11 @@ terminal, call:, session, call:terminal, src, get, response, websocket
 - ClearAllResponse
 - SessionRef
 - get_dashboard_summary
-- events_stream
+- health_check
 ## workflows
 - change system behavior
   read: __init__.py, dashboard.py, events.py
+- explore system subdirectories
+  index: apps/api/src/api/system/.ruff_cache/.pi-map.index.md
 ## dirty
 -
diff --git a/apps/api/src/api/system/terminal.py b/apps/api/src/api/system/terminal.py
index a868123..bb93e26 100644
--- a/apps/api/src/api/system/terminal.py
+++ b/apps/api/src/api/system/terminal.py
@@ -12,10 +12,12 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from starlette.websockets import WebSocketDisconnect
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models import TerminalSessionModel
-from src.models import ToolDefinitionManifest
-from src.models import ToolInstance
-from src.models import ToolType
+from src.models import (
+    TerminalSessionModel,
+    ToolDefinitionManifest,
+    ToolInstance,
+    ToolType,
+)
 from src.services.build.manifest_compiler import (
     deep_merge,
     get_manifest_container_user,
@@ -81,13 +83,19 @@ async def _resolve_container_user(
     if not tool_type or tool_type.definition_type != "manifest":
         return None
 
-    if not tool_type.manifest_id or not tool_type.manifest:
+    if not tool_type.manifest_id:
         return None
 
-    manifest = dict(tool_type.manifest.manifest)
-    if tool_type.manifest.base_definition_id:
+    manifest_def = await db_session.get(
+        ToolDefinitionManifest, tool_type.manifest_id
+    )
+    if not manifest_def:
+        return None
+
+    manifest = dict(manifest_def.manifest)
+    if manifest_def.base_definition_id:
         base_def = await db_session.get(
-            ToolDefinitionManifest, tool_type.manifest.base_definition_id
+            ToolDefinitionManifest, manifest_def.base_definition_id
         )
         if base_def:
             manifest = resolve_base(deep_merge(dict(base_def.manifest), manifest))
diff --git a/apps/api/tests/.pi-map.index.md b/apps/api/tests/.pi-map.index.md
index ac96aba..54c170a 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 FastAPI API integration tests.
+Provides shared pytest fixtures and test utilities for FastAPI application testing across the API test suite.
 ## parent
 index: apps/api/.pi-map.index.md
 map: apps/api/.pi-map.md
@@ -19,6 +19,12 @@ map: apps/api/.pi-map.md
 - apps/api/tests/system
   index: apps/api/tests/system/.pi-map.index.md
   map: apps/api/tests/system/.pi-map.md
+- apps/api/tests/test_routers
+  index: apps/api/tests/test_routers/.pi-map.index.md
+  map: apps/api/tests/test_routers/.pi-map.md
+- apps/api/tests/tools
+  index: apps/api/tests/tools/.pi-map.index.md
+  map: apps/api/tests/tools/.pi-map.md
 - apps/api/tests/unit
   index: apps/api/tests/unit/.pi-map.index.md
   map: apps/api/tests/unit/.pi-map.md
diff --git a/apps/api/tests/.pi-map.md b/apps/api/tests/.pi-map.md
index 5f64602..dec1f1e 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 FastAPI API integration tests.
+Provides shared pytest fixtures and test utilities for FastAPI application testing across the API test suite.
 ## files
-- conftest.py | Provides shared pytest fixtures for FastAPI integration testing, including test clients, database sessions, authenticated users, and admin users with SQLite in-memory database. | 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
+- conftest.py | Provides shared pytest fixtures including test clients, database sessions, authenticated clients, and test data for FastAPI application testing. | 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.testclient.TestClient
 ## arch
-Pytest fixture-based testing architecture with dependency injection overrides, SQLite in-memory database for test isolation, and pre-configured authenticated/admin user states.
+Standard pytest fixture pattern with dependency injection for test clients, database sessions, and authentication state management.
 ## 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 0cb371b..238a67a 100644
--- a/apps/api/tests/unit/.pi-map.index.md
+++ b/apps/api/tests/unit/.pi-map.index.md
@@ -2,12 +2,14 @@
 dir: apps/api/tests/unit
 
 ## role
-Contains unit tests for core API services and utilities, covering database migrations, configuration, Docker operations, Git integration, event handling, file management, health monitoring, manifest compilation, notifications, permissions, SSH keys, and terminal sessions.
+Unit test suite for the API backend, covering configuration, Docker services, Git operations, event bus, file/SSH/terminal utilities, 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
@@ -32,6 +34,7 @@ map: apps/api/tests/.pi-map.md
 - test_permission_fixer.py
 - test_readiness_probe.py
 - test_ssh_keys.py
+- test_terminal_container_user.py
 - test_terminal_session.py
 ## links
 index: apps/api/tests/unit/.pi-map.index.md
@@ -41,5 +44,7 @@ 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
 -
diff --git a/apps/api/tests/unit/.pi-map.md b/apps/api/tests/unit/.pi-map.md
index 433f2e3..2120be3 100644
--- a/apps/api/tests/unit/.pi-map.md
+++ b/apps/api/tests/unit/.pi-map.md
@@ -4,36 +4,37 @@ dir: apps/api/tests/unit
 index: apps/api/tests/unit/.pi-map.index.md
 
 ## role
-Contains unit tests for core API services and utilities, covering database migrations, configuration, Docker operations, Git integration, event handling, file management, health monitoring, manifest compilation, notifications, permissions, SSH keys, and terminal sessions.
+Unit test suite for the API backend, covering configuration, Docker services, Git operations, event bus, file/SSH/terminal utilities, monitoring, notifications, and manifest compilation.
 ## files
-- __init__.py | Provides a command to swap the position of two tmux panes within a window or between windows | dep: tmux, client, window, layout, cmd-find, cmd-parse, options
-- 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, func:test_remove_pi_agent_repo_mount_migration_imports() → 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
-- test_config.py | Unit tests for application configuration settings including database URLs, auth defaults, and cookie policies across environments. | exp: func:test_settings_default_database_url_uses_asyncpg(monkeypatch) → None, call:monkeypatch.delenv, call:Settings, func:test_build_database_url_uses_explicit_values() → None, call:build_database_url, func:test_settings_prefers_explicit_database_url_env(monkeypatch) → None, call:monkeypatch.setenv, call:Settings, func:test_auth_settings_have_secure_defaults() → None, call:Settings, call:settings.resolved_authentik_authorize_url.endswith, call:settings.resolved_authentik_token_url.endswith, call:settings.resolved_authentik_jwks_url.endswith, func:test_cookie_policy_is_strict_in_production(monkeypatch) → None, call:monkeypatch.setenv, call:Settings, func:test_cookie_policy_is_relaxed_for_local_dev(monkeypatch) → None, call:monkeypatch.setenv, call:Settings | dep: pytest, src.config, src.database
-- test_config_profile_resolver.py | Unit tests for config profile resolution, merging, and application, including inheritance, cycle detection, and mount normalization. | exp: class:TestMergeFunctions, method:test_merge_env_vars_basic(self) → None, call:_merge_env_vars, method:test_merge_env_vars_tracks_overrides(self) → None, call:_merge_env_vars, method:test_merge_runtime_hints_basic(self) → None, call:_merge_runtime_hints, method:test_merge_files_basic(self) → None, call:_merge_files, method:test_merge_mounts_basic(self) → None, call:_merge_mounts, method:test_merge_mounts_file_override(self) → None, call:_merge_mounts, call:ResolvedMount, method:test_merge_mounts_mode_conflict(self) → None, call:_merge_mounts, call:ResolvedMount, method:test_merge_git_mounts_basic(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_concatenate_same_repo_branch(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_dedup_same_mapping(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_different_repos(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_different_branches(self) → None, call:_merge_git_mounts, call:len, call:m.get, class:TestResolveProfile, class:TestApplyResolvedProfile, method:test_mounts_directory_not_individual_files(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:Path(volumes[0]["source"]).is_dir, call:(Path(volumes[0]["source"]) / "config.json").exists, call:(Path(volumes[0]["source"]) / "nested" / "file.txt").exists, method:test_directory_mount_target(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:Path, call:(Path(volumes[0]["source"]) / "z.json").exists, method:test_empty_mount_produces_no_volumes(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, method:test_home_expansion_in_directory_mount_target(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:(Path(volumes[0]["source"]) / "app.toml").exists, call:Path, method:test_readonly_mount_sets_readonly_flag(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:volumes[0].get, method:test_writable_mount_does_not_set_readonly_flag(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:volumes[0].get, class:TestCheckIncludeCycle | dep: uuid, pathlib, pytest, sqlalchemy.ext.asyncio, src.models.config.config_profile, src.services.config.config_profile_resolver
-- test_docker_build.py | Unit tests for a Docker image build service that verifies subprocess invocation, Dockerfile/context file writing, command structure, error handling, and path traversal prevention. | exp: class:TestBuildImage | dep: subprocess, tempfile, pathlib, unittest.mock, pytest, src.services.build.docker_build
-- test_docker_service.py | Unit tests for Docker service utilities including container ID/name retrieval and volume sorting by specificity. | exp: class:TestGetContainerId, class:TestGetContainerName, class:TestSortVolumesBySpecificity, method:test_parent_before_child(self) → None, call:sort_volumes_by_specificity, method:test_stable_sort_for_equal_depth(self) → None, call:sort_volumes_by_specificity, method:test_with_type_suffix(self) → None, call:sort_volumes_by_specificity, method:test_empty_list(self) → None, call:sort_volumes_by_specificity, method:test_single_volume(self) → None, call:sort_volumes_by_specificity, method:test_duplicate_target_warning(self, caplog) → None, call:caplog.at_level, call:sort_volumes_by_specificity | dep: unittest.mock, logging, src.services.docker.container, src.services.docker.compose, subprocess
-- test_event_bus.py | Unit tests for an instance event bus that validates publish/subscribe, error isolation, async callback support, and unsubscribe functionality. | exp: func:event_bus() → InstanceEventBus, call:InstanceEventBus, call:bus._reset_for_testing, func:sample_payload() → InstanceEventPayload, call:str, call:uuid.uuid4, func:test_publish_delivers_to_all_subscribers(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:event_bus.publish, call:len, func:callback_1(payload: InstanceEventPayload) → None, call:received.append, func:callback_2(payload: InstanceEventPayload) → None, call:received.append, func:callback_3(payload: InstanceEventPayload) → None, call:received.append, func:test_subscriber_exception_isolation(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:event_bus.publish, raise:RuntimeError, func:bad_callback(_payload: InstanceEventPayload) → None, raise:RuntimeError, func:good_callback(_payload: InstanceEventPayload) → None, call:received.append, func:test_unsubscribe_removes_callback(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:unsubscribe, call:event_bus.publish, func:callback(_payload: InstanceEventPayload) → None, call:received.append, func:test_publish_to_empty_subscriber_list(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:event_bus.publish, func:test_async_subscriber_supported(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:asyncio.sleep, call:received.append, call:event_bus.subscribe, call:event_bus.publish, func:async_callback(_payload: InstanceEventPayload) → None, call:asyncio.sleep, call:received.append, func:test_unsubscribe_all_clears_subscribers(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:event_bus.unsubscribe_all, call:event_bus.publish, func:callback(_payload: InstanceEventPayload) → None, call:received.append | dep: asyncio, uuid, typing, pytest, src.services.instance.event_bus
-- test_file_service.py | Unit tests for FileService validating directory listing, file read/write, binary rejection, and path traversal prevention. | exp: class:TestFileService, method:test_list_directory_empty(self, temp_workspace: Workspace), call:FileService, call:service.list_directory, method:test_list_directory_with_files(self, temp_workspace: Workspace), call:os.makedirs, call:os.path.join, call:open, call:f.write, call:FileService, call:service.list_directory, call:len, method:test_read_file(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:FileService, call:service.read_file, method:test_read_binary_file_rejected(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:FileService, call:pytest.raises, call:service.read_file, method:test_write_file(self, temp_workspace: Workspace), call:FileService, call:service.write_file, call:os.path.exists, call:os.path.join, call:open, call:f.read, method:test_path_escapes_workspace(self, temp_workspace: Workspace), call:FileService, call:pytest.raises, call:service.list_directory, func:temp_workspace(), call:tempfile.TemporaryDirectory, call:Workspace | dep: os, tempfile, pytest, src.models, src.services.shared.file_service, src.models.Workspace, src.services.shared.file_service.FileService
-- test_git_operations.py | Unit tests for GitOperations class covering status, commit, history, and branch operations | exp: class:TestGitOperationsStatus, method:test_status_clean(self, temp_workspace: Workspace), call:GitOperations, call:asyncio.run, call:git.status, method:test_status_modified(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.status, method:test_status_untracked(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.status, class:TestGitOperationsCommit, method:test_commit_stages_and_commits(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.commit, call:git.status, call:git.history, method:test_commit_fails_without_changes(self, temp_workspace: Workspace), call:GitOperations, call:pytest.raises, call:asyncio.run, call:git.commit, class:TestGitOperationsHistory, method:test_history_returns_commits(self, temp_workspace: Workspace), call:GitOperations, call:asyncio.run, call:git.history, call:len, method:test_history_filters_by_path(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.commit, call:git.history, call:len, class:TestGitOperationsBranches, method:test_branches_lists_main(self, temp_workspace: Workspace), call:GitOperations, call:asyncio.run, call:git.branches, method:test_checkout_switches_branch(self, temp_workspace: Workspace), call:_run_git, call:GitOperations, call:asyncio.run, call:git.checkout, call:git.status, func:_run_git(*args: str, cwd: str) → None, call:subprocess.run, func:temp_workspace(), call:tempfile.TemporaryDirectory, call:_run_git, call:os.path.join, call:open, call:f.write, call:Workspace | dep: asyncio, os, subprocess, tempfile, pytest, src.models, src.services.git.git_operations, src.models.Workspace, src.services.git.git_operations.GitOperations
-- test_git_service.py | Unit tests for GitService covering clone, fetch, pull, and branch existence checks via mocked subprocess calls | exp: class:TestGitServiceClone, class:TestGitServiceFetch, class:TestGitServicePull, class:TestGitServiceBranchExistsRemotely, method:test_branch_exists(self), call:MagicMock, call:patch, call:GitService.branch_exists_remotely, call:mock_run.assert_called_once_with, method:test_branch_not_exists(self), call:MagicMock, call:patch, call:GitService.branch_exists_remotely, method:test_ls_remote_fails(self), call:MagicMock, call:patch, call:GitService.branch_exists_remotely | dep: asyncio, unittest.mock, pytest, src.services.git.git_service
-- test_git_url_parser.py | Unit tests for git URL parsing utilities that validate extraction, validation, and parsing of various GitHub, GitLab, and Bitbucket URL formats. | exp: class:TestExtractBaseRepoUrl, method:test_github_tree_url(self), call:extract_base_repo_url, method:test_github_blob_url(self), call:extract_base_repo_url, method:test_github_pull_url(self), call:extract_base_repo_url, method:test_github_issues_url(self), call:extract_base_repo_url, method:test_github_valid_url(self), call:extract_base_repo_url, method:test_github_url_with_query_params(self), call:extract_base_repo_url, method:test_gitlab_tree_url(self), call:extract_base_repo_url, method:test_gitlab_blob_url(self), call:extract_base_repo_url, method:test_gitlab_merge_request_url(self), call:extract_base_repo_url, method:test_gitlab_valid_url(self), call:extract_base_repo_url, method:test_bitbucket_src_url(self), call:extract_base_repo_url, method:test_bitbucket_valid_url(self), call:extract_base_repo_url, method:test_ssh_url(self), call:extract_base_repo_url, method:test_ssh_url_without_git_suffix(self), call:extract_base_repo_url, method:test_invalid_url(self), call:extract_base_repo_url, method:test_empty_url(self), call:extract_base_repo_url, class:TestIsValidCloneUrl, method:test_valid_ssh_url(self), call:is_valid_clone_url, method:test_valid_https_url(self), call:is_valid_clone_url, method:test_browser_url(self), call:is_valid_clone_url, method:test_url_without_git_suffix(self), call:is_valid_clone_url, method:test_invalid_url(self), call:is_valid_clone_url, class:TestParseGitUrl, method:test_valid_git_url(self), call:parse_git_url, method:test_browser_url(self), call:parse_git_url, method:test_invalid_url(self), call:parse_git_url, method:test_empty_url(self), call:parse_git_url, method:test_ssh_url(self), call:parse_git_url | dep: src.utils.git_url_parser, pytest
-- test_health_monitor.py | Unit tests for HealthMonitor state-transition logic covering container crash detection, tunnel failure detection, recovery detection, write deduplication, and exception resilience. | exp: func:event_bus() → InstanceEventBus, call:InstanceEventBus, call:bus._reset_for_testing, func:health_monitor(event_bus: InstanceEventBus) → HealthMonitor, call:HealthMonitor, func:_create_running_instance(db_session) → ToolInstance, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, call:ToolInstance, func:test_detects_container_crash(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:events_captured.append, call:event_bus.subscribe, call:patch, call:health_monitor._check_instance, call:db_session.refresh, call:len, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_detects_tunnel_failure(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:events_captured.append, call:event_bus.subscribe, call:patch, call:health_monitor._check_instance, call:db_session.refresh, call:len, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_detects_recovery(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:db_session.commit, call:HealthSnapshot, call:events_captured.append, call:event_bus.subscribe, call:patch, call:health_monitor._check_instance, call:db_session.refresh, call:len, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_skips_writes_when_no_state_change(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:HealthSnapshot, call:patch, call:health_monitor._check_instance, call:db_session.execute, call:select(HealthCheck).where, call:len, call:result.scalars().all, func:test_docker_exception_resilience(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:events_captured.append, call:event_bus.subscribe, call:patch, call:RuntimeError, call:health_monitor._check_instance, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one_or_none, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_monitor_start_stop(health_monitor: HealthMonitor) → None, call:health_monitor.start, call:task.done, call:health_monitor.stop, call:suppress, call:task.cancelled | dep: asyncio, uuid, contextlib, unittest.mock, pytest, sqlalchemy, src.models.system.health_check, src.models.tool.tool_instance, src.models.user.user, src.services.instance.event_bus, src.services.instance.health_monitor
-- test_home_path_expansion.py | Unit tests for tilde and $HOME expansion in container paths, and manifest-based 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 the tool instance service covering compose file modification, repository mount naming, profile/git mount stacking, and manifest instance preparation. | 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, class:TestGetRepositoryMountName, method:test_uses_project_name(self), call:MagicMock, call:_get_repository_mount_name, method:test_slugifies_project_name(self), call:MagicMock, call:_get_repository_mount_name, class:TestStackProfileMountsWithGitMounts, method:test_exact_overlap_merges_profile_files_into_git_source(self, tmp_path) → None, call:git_source.mkdir, call:(git_source / "existing.txt").write_text, call:profile_source.mkdir, call:(profile_source / "settings.json").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, call:(git_source / "existing.txt").read_text, call:(git_source / "settings.json").read_text, method:test_descendant_overlap_copies_into_subdirectory(self, tmp_path) → None, call:git_source.mkdir, call:(git_source / "README").write_text, call:profile_source.mkdir, call:(profile_source / "settings.json").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, call:(git_source / "agent" / "settings.json").read_text, call:(git_source / "README").read_text, method:test_non_overlapping_mounts_left_untouched(self, tmp_path) → None, call:git_source.mkdir, call:profile_source.mkdir, call:(profile_source / "config").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, method:test_git_source_file_does_not_consume_profile_mount(self, tmp_path) → None, call:git_source.write_text, call:profile_source.mkdir, call:(profile_source / "settings.json").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, method:test_profile_source_file_copied_into_git_source(self, tmp_path) → None, call:git_source.mkdir, call:profile_source.write_text, call:str, call:_stack_profile_mounts_with_git_mounts, call:(git_source / "settings.json").read_text, class:Result, func:test_prepare_manifest_instance_uses_workspace_path_basename(), call:MagicMock, call:AsyncMock, call:Result, call:prepare_manifest_instance, func:session_get(model, obj_id), func:fake_run(cmd), call:Result | dep: unittest.mock, pytest, src.services.tool.instance_service, subprocess, src.services.tool
+- __init__.py | Empty package initialization file that marks a directory as a Python package.
+- test_alembic_migrations.py | Verifies the structure, importability, and metadata of specific Alembic migration files without requiring a database connection. | 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, func:test_remove_pi_agent_repo_mount_migration_imports() → 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, pathlib.Path
+- test_config.py | Unit tests verifying configuration settings including database URLs, auth defaults, and environment-specific cookie policies. | exp: func:test_settings_default_database_url_uses_asyncpg(monkeypatch) → None, call:monkeypatch.delenv, call:Settings, func:test_build_database_url_uses_explicit_values() → None, call:build_database_url, func:test_settings_prefers_explicit_database_url_env(monkeypatch) → None, call:monkeypatch.setenv, call:Settings, func:test_auth_settings_have_secure_defaults() → None, call:Settings, call:settings.resolved_authentik_authorize_url.endswith, call:settings.resolved_authentik_token_url.endswith, call:settings.resolved_authentik_jwks_url.endswith, func:test_cookie_policy_is_strict_in_production(monkeypatch) → None, call:monkeypatch.setenv, call:Settings, func:test_cookie_policy_is_relaxed_for_local_dev(monkeypatch) → None, call:monkeypatch.setenv, call:Settings | dep: pytest, src.config, src.database, src.config.Settings, src.database.build_database_url
+- test_config_profile_resolver.py | Tests config profile resolution logic including merge functions, profile inheritance with includes, cycle detection, and git mount normalization. | exp: class:TestMergeFunctions, method:test_merge_env_vars_basic(self) → None, call:_merge_env_vars, method:test_merge_env_vars_tracks_overrides(self) → None, call:_merge_env_vars, method:test_merge_runtime_hints_basic(self) → None, call:_merge_runtime_hints, method:test_merge_files_basic(self) → None, call:_merge_files, method:test_merge_mounts_basic(self) → None, call:_merge_mounts, method:test_merge_mounts_file_override(self) → None, call:_merge_mounts, call:ResolvedMount, method:test_merge_mounts_mode_conflict(self) → None, call:_merge_mounts, call:ResolvedMount, method:test_merge_git_mounts_basic(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_concatenate_same_repo_branch(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_dedup_same_mapping(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_different_repos(self) → None, call:_merge_git_mounts, call:len, method:test_merge_git_mounts_different_branches(self) → None, call:_merge_git_mounts, call:len, call:m.get, class:TestResolveProfile, class:TestApplyResolvedProfile, method:test_mounts_directory_not_individual_files(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:Path(volumes[0]["source"]).is_dir, call:(Path(volumes[0]["source"]) / "config.json").exists, call:(Path(volumes[0]["source"]) / "nested" / "file.txt").exists, method:test_directory_mount_target(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:Path, call:(Path(volumes[0]["source"]) / "z.json").exists, method:test_empty_mount_produces_no_volumes(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, method:test_home_expansion_in_directory_mount_target(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:(Path(volumes[0]["source"]) / "app.toml").exists, call:Path, method:test_readonly_mount_sets_readonly_flag(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:volumes[0].get, method:test_writable_mount_does_not_set_readonly_flag(self, tmp_path) → None, call:ResolvedProfile, call:uuid.uuid4, call:ResolvedMount, call:apply_resolved_profile, call:str, call:len, call:volumes[0].get, class:TestCheckIncludeCycle | dep: uuid, pathlib, pytest, sqlalchemy.ext.asyncio, src.models.config.config_profile, src.services.config.config_profile_resolver, pathlib.Path, sqlalchemy.ext.asyncio.AsyncSession
+- test_docker_build.py | Unit tests for the `build_image` Docker build service function, verifying successful builds, error handling, file writing, and security. | exp: class:TestBuildImage | dep: subprocess, tempfile, pathlib, unittest.mock, pytest, src.services.build.docker_build, pathlib.Path
+- test_docker_service.py | Unit tests for Docker container utilities (ID/name lookup) and volume sorting by mount specificity. | exp: class:TestGetContainerId, class:TestGetContainerName, class:TestSortVolumesBySpecificity, method:test_parent_before_child(self) → None, call:sort_volumes_by_specificity, method:test_stable_sort_for_equal_depth(self) → None, call:sort_volumes_by_specificity, method:test_with_type_suffix(self) → None, call:sort_volumes_by_specificity, method:test_empty_list(self) → None, call:sort_volumes_by_specificity, method:test_single_volume(self) → None, call:sort_volumes_by_specificity, method:test_duplicate_target_warning(self, caplog) → None, call:caplog.at_level, call:sort_volumes_by_specificity | dep: unittest.mock, logging, src.services.docker.container, src.services.docker.compose, subprocess
+- test_event_bus.py | Unit tests for the InstanceEventBus pub/sub system, verifying event delivery, subscriber isolation, unsubscription, and async callback support. | exp: func:event_bus() → InstanceEventBus, call:InstanceEventBus, call:bus._reset_for_testing, func:sample_payload() → InstanceEventPayload, call:str, call:uuid.uuid4, func:test_publish_delivers_to_all_subscribers(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:event_bus.publish, call:len, func:callback_1(payload: InstanceEventPayload) → None, call:received.append, func:callback_2(payload: InstanceEventPayload) → None, call:received.append, func:callback_3(payload: InstanceEventPayload) → None, call:received.append, func:test_subscriber_exception_isolation(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:event_bus.publish, raise:RuntimeError, func:bad_callback(_payload: InstanceEventPayload) → None, raise:RuntimeError, func:good_callback(_payload: InstanceEventPayload) → None, call:received.append, func:test_unsubscribe_removes_callback(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:unsubscribe, call:event_bus.publish, func:callback(_payload: InstanceEventPayload) → None, call:received.append, func:test_publish_to_empty_subscriber_list(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:event_bus.publish, func:test_async_subscriber_supported(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:asyncio.sleep, call:received.append, call:event_bus.subscribe, call:event_bus.publish, func:async_callback(_payload: InstanceEventPayload) → None, call:asyncio.sleep, call:received.append, func:test_unsubscribe_all_clears_subscribers(event_bus: InstanceEventBus, sample_payload: InstanceEventPayload) → None, call:received.append, call:event_bus.subscribe, call:event_bus.unsubscribe_all, call:event_bus.publish, func:callback(_payload: InstanceEventPayload) → None, call:received.append | dep: asyncio, uuid, typing, pytest, src.services.instance.event_bus
+- test_file_service.py | Unit tests for FileService covering directory listing, file reading/writing, binary file rejection, and path traversal prevention. | exp: class:TestFileService, method:test_list_directory_empty(self, temp_workspace: Workspace), call:FileService, call:service.list_directory, method:test_list_directory_with_files(self, temp_workspace: Workspace), call:os.makedirs, call:os.path.join, call:open, call:f.write, call:FileService, call:service.list_directory, call:len, method:test_read_file(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:FileService, call:service.read_file, method:test_read_binary_file_rejected(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:FileService, call:pytest.raises, call:service.read_file, method:test_write_file(self, temp_workspace: Workspace), call:FileService, call:service.write_file, call:os.path.exists, call:os.path.join, call:open, call:f.read, method:test_path_escapes_workspace(self, temp_workspace: Workspace), call:FileService, call:pytest.raises, call:service.list_directory, func:temp_workspace(), call:tempfile.TemporaryDirectory, call:Workspace | dep: os, tempfile, pytest, src.models, src.services.shared.file_service, src.models.Workspace, src.services.shared.file_service.FileService
+- test_git_operations.py | Unit tests for GitOperations methods including status, commit, history, and branch operations using temporary git repositories. | exp: class:TestGitOperationsStatus, method:test_status_clean(self, temp_workspace: Workspace), call:GitOperations, call:asyncio.run, call:git.status, method:test_status_modified(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.status, method:test_status_untracked(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.status, class:TestGitOperationsCommit, method:test_commit_stages_and_commits(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.commit, call:git.status, call:git.history, method:test_commit_fails_without_changes(self, temp_workspace: Workspace), call:GitOperations, call:pytest.raises, call:asyncio.run, call:git.commit, class:TestGitOperationsHistory, method:test_history_returns_commits(self, temp_workspace: Workspace), call:GitOperations, call:asyncio.run, call:git.history, call:len, method:test_history_filters_by_path(self, temp_workspace: Workspace), call:open, call:os.path.join, call:f.write, call:GitOperations, call:asyncio.run, call:git.commit, call:git.history, call:len, class:TestGitOperationsBranches, method:test_branches_lists_main(self, temp_workspace: Workspace), call:GitOperations, call:asyncio.run, call:git.branches, method:test_checkout_switches_branch(self, temp_workspace: Workspace), call:_run_git, call:GitOperations, call:asyncio.run, call:git.checkout, call:git.status, func:_run_git(*args: str, cwd: str) → None, call:subprocess.run, func:temp_workspace(), call:tempfile.TemporaryDirectory, call:_run_git, call:os.path.join, call:open, call:f.write, call:Workspace | dep: asyncio, os, subprocess, tempfile, pytest, src.models, src.services.git.git_operations, src.models.Workspace, src.services.git.git_operations.GitOperations
+- test_git_service.py | Unit tests for GitService methods including clone, fetch, pull, and branch_exists_remotely operations. | exp: class:TestGitServiceClone, class:TestGitServiceFetch, class:TestGitServicePull, class:TestGitServiceBranchExistsRemotely, method:test_branch_exists(self), call:MagicMock, call:patch, call:GitService.branch_exists_remotely, call:mock_run.assert_called_once_with, method:test_branch_not_exists(self), call:MagicMock, call:patch, call:GitService.branch_exists_remotely, method:test_ls_remote_fails(self), call:MagicMock, call:patch, call:GitService.branch_exists_remotely | dep: asyncio, unittest.mock, pytest, src.services.git.git_service, src.services.git.git_service.GitService
+- test_git_url_parser.py | Tests for git URL parsing utilities including base URL extraction, clone URL validation, and full URL parsing across multiple Git hosting platforms. | exp: class:TestExtractBaseRepoUrl, method:test_github_tree_url(self), call:extract_base_repo_url, method:test_github_blob_url(self), call:extract_base_repo_url, method:test_github_pull_url(self), call:extract_base_repo_url, method:test_github_issues_url(self), call:extract_base_repo_url, method:test_github_valid_url(self), call:extract_base_repo_url, method:test_github_url_with_query_params(self), call:extract_base_repo_url, method:test_gitlab_tree_url(self), call:extract_base_repo_url, method:test_gitlab_blob_url(self), call:extract_base_repo_url, method:test_gitlab_merge_request_url(self), call:extract_base_repo_url, method:test_gitlab_valid_url(self), call:extract_base_repo_url, method:test_bitbucket_src_url(self), call:extract_base_repo_url, method:test_bitbucket_valid_url(self), call:extract_base_repo_url, method:test_ssh_url(self), call:extract_base_repo_url, method:test_ssh_url_without_git_suffix(self), call:extract_base_repo_url, method:test_invalid_url(self), call:extract_base_repo_url, method:test_empty_url(self), call:extract_base_repo_url, class:TestIsValidCloneUrl, method:test_valid_ssh_url(self), call:is_valid_clone_url, method:test_valid_https_url(self), call:is_valid_clone_url, method:test_browser_url(self), call:is_valid_clone_url, method:test_url_without_git_suffix(self), call:is_valid_clone_url, method:test_invalid_url(self), call:is_valid_clone_url, class:TestParseGitUrl, method:test_valid_git_url(self), call:parse_git_url, method:test_browser_url(self), call:parse_git_url, method:test_invalid_url(self), call:parse_git_url, method:test_empty_url(self), call:parse_git_url, method:test_ssh_url(self), call:parse_git_url | dep: src.utils.git_url_parser
+- test_health_monitor.py | Unit tests for HealthMonitor state-transition logic, validating container crash detection, tunnel failure handling, recovery detection, and resilience to Docker exceptions. | exp: func:event_bus() → InstanceEventBus, call:InstanceEventBus, call:bus._reset_for_testing, func:health_monitor(event_bus: InstanceEventBus) → HealthMonitor, call:HealthMonitor, func:_create_running_instance(db_session) → ToolInstance, call:User, call:uuid.uuid4, call:db_session.add, call:db_session.commit, call:ToolInstance, func:test_detects_container_crash(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:events_captured.append, call:event_bus.subscribe, call:patch, call:health_monitor._check_instance, call:db_session.refresh, call:len, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_detects_tunnel_failure(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:events_captured.append, call:event_bus.subscribe, call:patch, call:health_monitor._check_instance, call:db_session.refresh, call:len, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_detects_recovery(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:db_session.commit, call:HealthSnapshot, call:events_captured.append, call:event_bus.subscribe, call:patch, call:health_monitor._check_instance, call:db_session.refresh, call:len, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_skips_writes_when_no_state_change(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:HealthSnapshot, call:patch, call:health_monitor._check_instance, call:db_session.execute, call:select(HealthCheck).where, call:len, call:result.scalars().all, func:test_docker_exception_resilience(db_session, event_bus: InstanceEventBus, health_monitor: HealthMonitor) → None, call:_create_running_instance, call:events_captured.append, call:event_bus.subscribe, call:patch, call:RuntimeError, call:health_monitor._check_instance, call:db_session.execute, call:select(HealthCheck).where, call:result.scalar_one_or_none, func:capture_event(payload: InstanceEventPayload) → None, call:events_captured.append, func:test_monitor_start_stop(health_monitor: HealthMonitor) → None, call:health_monitor.start, call:task.done, call:health_monitor.stop, call:suppress, call:task.cancelled | dep: asyncio, uuid, contextlib, unittest.mock, pytest, sqlalchemy, src.models.system.health_check, src.models.tool.tool_instance, src.models.user.user, src.services.instance.event_bus, src.services.instance.health_monitor
+- test_home_path_expansion.py | Unit tests verifying tilde (~) and $HOME path expansion and home directory resolution from container manifests. | 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 tool instance service functions including compose file modification, repository mount name generation, profile/git mount stacking, and manifest instance preparation. | 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, class:TestGetRepositoryMountName, method:test_uses_project_name(self), call:MagicMock, call:_get_repository_mount_name, method:test_slugifies_project_name(self), call:MagicMock, call:_get_repository_mount_name, class:TestStackProfileMountsWithGitMounts, method:test_exact_overlap_merges_profile_files_into_git_source(self, tmp_path) → None, call:git_source.mkdir, call:(git_source / "existing.txt").write_text, call:profile_source.mkdir, call:(profile_source / "settings.json").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, call:(git_source / "existing.txt").read_text, call:(git_source / "settings.json").read_text, method:test_descendant_overlap_copies_into_subdirectory(self, tmp_path) → None, call:git_source.mkdir, call:(git_source / "README").write_text, call:profile_source.mkdir, call:(profile_source / "settings.json").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, call:(git_source / "agent" / "settings.json").read_text, call:(git_source / "README").read_text, method:test_non_overlapping_mounts_left_untouched(self, tmp_path) → None, call:git_source.mkdir, call:profile_source.mkdir, call:(profile_source / "config").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, method:test_git_source_file_does_not_consume_profile_mount(self, tmp_path) → None, call:git_source.write_text, call:profile_source.mkdir, call:(profile_source / "settings.json").write_text, call:str, call:_stack_profile_mounts_with_git_mounts, method:test_profile_source_file_copied_into_git_source(self, tmp_path) → None, call:git_source.mkdir, call:profile_source.write_text, call:str, call:_stack_profile_mounts_with_git_mounts, call:(git_source / "settings.json").read_text, class:Result, func:test_prepare_manifest_instance_uses_workspace_path_basename(), call:MagicMock, call:AsyncMock, call:Result, call:prepare_manifest_instance, func:session_get(model, obj_id), func:fake_run(cmd), call:Result, func:test_create_tool_instance_resolves_project_when_display_name_given(monkeypatch, tmp_path), call:uuid.uuid4, call:MagicMock, call:getattr, call:AsyncMock, call:monkeypatch.setattr, call:str, call:CreateInstanceRequest, call:instance_service.create_tool_instance, func:session_get(model, _obj_id), call:getattr | dep: uuid, unittest.mock, pytest, src.services.tool.instance_service, subprocess, src.services.tool, src.schemas.tool
 - 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_project_directory(self) → None, call:compile_dockerfile, method:test_project_directory_created(self) → None, call:compile_dockerfile, method:test_runtime_workspace_not_baked_into_image(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_project_directory(self) → None, call:compile_entrypoint, method:test_entrypoint_removes_stale_placeholder_directory(self) → None, call:compile_entrypoint, method:test_entrypoint_does_not_create_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, func:test_compile_dockerfile_starts_as_root_and_drops_privileges() → None, call:compile_dockerfile, call:compile_entrypoint, func:test_compile_compose_does_not_pin_root_user() → None, call:compile_compose, func:test_get_manifest_container_user_returns_name() → None, call:get_manifest_container_user, func:test_get_manifest_container_user_falls_back_to_uid_gid() → None, call:get_manifest_container_user, func:test_get_manifest_container_user_returns_none_without_user() → None, call:get_manifest_container_user | dep: pytest, src.services.build.manifest_compiler
-- test_migration_metadata.py | Validates Alembic migration files by dynamically importing them and verifying 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, ownership validation, and bulk actions on user notifications. | 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, Notification, User, NotificationService
-- test_notifications_api_routes.py | Tests FastAPI route ordering to ensure DELETE /notifications matches the bulk clear endpoint before the parameterized DELETE /notifications/{id} endpoint. | exp: func:test_delete_notifications_route_order() → None, call:FastAPI, call:app.include_router, call:TestClient, call:client.delete | dep: fastapi, fastapi.testclient, src.api.system.notifications
-- test_permission_fixer.py | Unit tests for a Docker container permission fixer that applies chown/chmod/file_mode to mounts and SSH directories. | exp: class:TestApplyMountPermissions, class:TestRunInContainer, class:TestApplySshPermissions, class:TestCheckRootUserAvailable | dep: unittest.mock, pytest, src.services.shared.permission_fixer, subprocess
-- test_readiness_probe.py | Unit tests for a Docker container readiness probe service that executes commands with retry logic and timeout handling | exp: class:TestExecuteProbe, class:TestIntegrationScenarios | dep: unittest.mock, src.services.shared.readiness_probe, subprocess
-- test_ssh_keys.py | Unit tests for SSH key file preparation functionality including file creation, permissions, ownership, and error handling. | exp: class:TestPrepareSshKeyFiles | dep: os, pathlib, unittest.mock, pytest, src.services.shared.ssh_keys
-- test_terminal_session.py | Unit tests for TerminalSession verifying docker exec command construction with/without container user flag | exp: func:test_start_passes_container_user_to_docker_exec() → None, call:TerminalSession, call:str, call:uuid.uuid4, call:patch, call:AsyncMock, call:session.start, call:args.index, func:test_start_omits_user_when_not_configured() → None, call:TerminalSession, call:str, call:uuid.uuid4, call:patch, call:AsyncMock, call:session.start | dep: uuid, unittest.mock, pytest, src.services.terminal.terminal_session, pty, asyncio, os
+- test_migration_metadata.py | Unit tests that dynamically load and validate Alembic migration files for correct table definitions and revision chains. | 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
+- test_monitoring_models.py | Tests creation, persistence, and querying of monitoring models (InstanceEvent and HealthCheck) with related User and ToolInstance fixtures. | 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 creation, listing, filtering, reading, dismissing, and ownership validation of user notifications. | 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
+- test_notifications_api_routes.py | Tests that the FastAPI route ordering for notifications is correct so the bulk DELETE endpoint doesn't get intercepted by the single-item path parameter route. | exp: func:test_delete_notifications_route_order() → None, call:FastAPI, call:app.include_router, call:TestClient, call:client.delete | dep: fastapi, fastapi.testclient, src.api.system.notifications, FastAPI, TestClient
+- test_permission_fixer.py | Unit tests for the permission fixer module that validates Docker container permission management (chown/chmod operations on mounts and SSH directories). | exp: class:TestApplyMountPermissions, class:TestRunInContainer, class:TestApplySshPermissions, class:TestCheckRootUserAvailable | dep: unittest.mock, pytest, src.services.shared.permission_fixer, subprocess
+- test_readiness_probe.py | Unit tests for the readiness probe service that validates container health checks via Docker exec commands with retry logic. | exp: class:TestExecuteProbe, class:TestIntegrationScenarios | dep: unittest.mock, src.services.shared.readiness_probe
+- test_ssh_keys.py | Unit tests for the `prepare_ssh_key_files` function, verifying file creation, permissions, ownership setting, and error handling. | exp: class:TestPrepareSshKeyFiles | dep: os, pathlib, unittest.mock, pytest, src.services.shared.ssh_keys, pathlib.Path
+- test_terminal_container_user.py | Unit tests for resolving container user from tool type definitions, handling legacy tools, manifest-based tools, base definition inheritance, and missing definitions. | exp: func:test_resolve_container_user_legacy_tool_type(), call:MagicMock, call:AsyncMock, call:_resolve_container_user, call:session.get.assert_awaited_once, func:test_resolve_container_user_manifest_no_manifest_id(), call:MagicMock, call:AsyncMock, call:_resolve_container_user, func:test_resolve_container_user_manifest_with_user(), call:MagicMock, call:AsyncMock, call:_resolve_container_user, func:session_get(model, obj_id), func:test_resolve_container_user_manifest_with_base_definition(), call:MagicMock, call:AsyncMock, call:_resolve_container_user, func:session_get(model, obj_id), func:test_resolve_container_user_missing_manifest_definition(), call:MagicMock, call:AsyncMock, call:_resolve_container_user, func:session_get(model, obj_id) | dep: unittest.mock, pytest, src.api.system.terminal, src.api.system.terminal._resolve_container_user
+- test_terminal_session.py | Unit tests verifying TerminalSession passes container_user to docker exec --user flag when set, and omits it when not configured. | exp: func:test_start_passes_container_user_to_docker_exec() → None, call:TerminalSession, call:str, call:uuid.uuid4, call:patch, call:AsyncMock, call:session.start, call:args.index, func:test_start_omits_user_when_not_configured() → None, call:TerminalSession, call:str, call:uuid.uuid4, call:patch, call:AsyncMock, call:session.start | dep: uuid, unittest.mock, pytest, src.services.terminal.terminal_session
 ## arch
-Follows pytest-based unit testing architecture with heavy use of mocking (subprocess, filesystem, database) to test services in isolation; tests are organized by service/module with descriptive naming; employs parametrization and fixture-based setup for testing edge cases, error conditions, and path traversal prevention across infrastructure and security-critical components.
+pytest-based unit testing with fixtures for temporary resources (git repos, Docker mocks), heavy use of mocking for external dependencies (Docker, databases), and parameterized tests for cross-platform/git-hosting scenarios.
 ## tags
-test, url, call:, git, call:notification, mounts, home, merge
+test, url, call:, git, user, call:notification, container, mounts
 ## symbols
 - TestMergeFunctions
 - TestResolveProfile
@@ -48,5 +49,7 @@ test, url, call:, git, call:notification, mounts, home, merge
   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
 -
diff --git a/apps/api/tests/unit/test_terminal_container_user.py b/apps/api/tests/unit/test_terminal_container_user.py
new file mode 100644
index 0000000..51b220a
--- /dev/null
+++ b/apps/api/tests/unit/test_terminal_container_user.py
@@ -0,0 +1,143 @@
+"""Unit tests for terminal container-user resolution."""
+
+from unittest.mock import AsyncMock, MagicMock
+
+import pytest
+
+from src.api.system.terminal import _resolve_container_user
+
+
+@pytest.mark.unit
+async def test_resolve_container_user_legacy_tool_type():
+    """Legacy tools have no manifest user."""
+    tool_type = MagicMock()
+    tool_type.definition_type = "legacy"
+    tool_type.manifest_id = None
+
+    instance = MagicMock()
+    instance.tool_type_id = "tool-type-uuid"
+
+    session = AsyncMock()
+    session.get = AsyncMock(return_value=tool_type)
+
+    result = await _resolve_container_user(session, instance)
+
+    assert result is None
+    session.get.assert_awaited_once()
+
+
+@pytest.mark.unit
+async def test_resolve_container_user_manifest_no_manifest_id():
+    """Manifest-based tools without a manifest_id return None."""
+    tool_type = MagicMock()
+    tool_type.definition_type = "manifest"
+    tool_type.manifest_id = None
+
+    instance = MagicMock()
+    instance.tool_type_id = "tool-type-uuid"
+
+    session = AsyncMock()
+    session.get = AsyncMock(return_value=tool_type)
+
+    result = await _resolve_container_user(session, instance)
+
+    assert result is None
+
+
+@pytest.mark.unit
+async def test_resolve_container_user_manifest_with_user():
+    """Manifest-based tools resolve the declared container user."""
+    manifest_id = "manifest-uuid"
+
+    tool_type = MagicMock()
+    tool_type.definition_type = "manifest"
+    tool_type.manifest_id = manifest_id
+
+    manifest_def = MagicMock()
+    manifest_def.manifest = {"user": {"name": "dev", "uid": 1000, "gid": 1000}}
+    manifest_def.base_definition_id = None
+
+    instance = MagicMock()
+    instance.tool_type_id = "tool-type-uuid"
+
+    session = AsyncMock()
+
+    async def session_get(model, obj_id):
+        if obj_id == "tool-type-uuid":
+            return tool_type
+        if obj_id == manifest_id:
+            return manifest_def
+        return None
+
+    session.get.side_effect = session_get
+
+    result = await _resolve_container_user(session, instance)
+
+    assert result == "dev"
+
+
+@pytest.mark.unit
+async def test_resolve_container_user_manifest_with_base_definition():
+    """Base-definition users are inherited and overridden by tool manifests."""
+    base_id = "base-uuid"
+    manifest_id = "manifest-uuid"
+
+    tool_type = MagicMock()
+    tool_type.definition_type = "manifest"
+    tool_type.manifest_id = manifest_id
+
+    manifest_def = MagicMock()
+    manifest_def.manifest = {"user": {"name": "override", "uid": 1001, "gid": 1001}}
+    manifest_def.base_definition_id = base_id
+
+    base_def = MagicMock()
+    base_def.manifest = {
+        "base_image": "ubuntu:24.04",
+        "user": {"name": "base", "uid": 1000, "gid": 1000},
+    }
+
+    instance = MagicMock()
+    instance.tool_type_id = "tool-type-uuid"
+
+    session = AsyncMock()
+
+    async def session_get(model, obj_id):
+        if obj_id == "tool-type-uuid":
+            return tool_type
+        if obj_id == manifest_id:
+            return manifest_def
+        if obj_id == base_id:
+            return base_def
+        return None
+
+    session.get.side_effect = session_get
+
+    result = await _resolve_container_user(session, instance)
+
+    assert result == "override"
+
+
+@pytest.mark.unit
+async def test_resolve_container_user_missing_manifest_definition():
+    """A manifest_id pointing to a missing definition returns None."""
+    manifest_id = "manifest-uuid"
+
+    tool_type = MagicMock()
+    tool_type.definition_type = "manifest"
+    tool_type.manifest_id = manifest_id
+
+    instance = MagicMock()
+    instance.tool_type_id = "tool-type-uuid"
+
+    session = AsyncMock()
+
+    async def session_get(model, obj_id):
+        if obj_id == "tool-type-uuid":
+            return tool_type
+        return None
+
+    session.get.side_effect = session_get
+
+    result = await _resolve_container_user(session, instance)
+
+    assert result is None