feat: add config profiles data model and migrations

- Add ConfigProfile model with user ownership, name, description
- Add ConfigInclude model for ordered profile self-references
- Add ConfigMount model for mount/file definitions
- Add selected_profile_id to ToolInstance for per-instance profile selection
- Add default profile properties to UserConfig JSONB config
- Create Alembic migration 0013 for new tables and columns
- Register new models in models/__init__.py
- Mark config_folders.is_active as deprecated
- Add migration metadata test

Quality gates: syntax check passed (all files parse successfully)
OpenSpec: add-config-profiles task 1.1

.env.example

@@ -6,10 +6,9 @@ POSTGRES_DB=headquarter
 # Redis Configuration
 REDIS_URL=redis://redis:6379/0
 
-# JWT Configuration
-JWT_SECRET=change-me-in-production
-JWT_ALGORITHM=HS256
-JWT_EXPIRATION_HOURS=24
+# Session Configuration
+SESSION_SECRET=change-me-in-production
+SESSION_TTL_HOURS=24
 
 # Application Configuration
 APP_ENV=development
@@ -37,9 +36,6 @@ AUTHENTIK_APPLICATION_SLUG=headquarter-web
 # Override Authentik URLs if they differ from the default pattern
 # AUTHENTIK_AUTHORIZE_URL=https://authentik.example.com/application/o/authorize/
 # AUTHENTIK_TOKEN_URL=https://authentik.example.com/application/o/token/
-# AUTHENTIK_JWKS_URL=https://authentik.example.com/application/o/headquarter-web/jwks/
-# AUTHENTIK_ISSUER=https://authentik.example.com/application/o/headquarter-web/
-AUTHENTIK_AUDIENCE=headquarter-web
 
 # Frontend Configuration
 VITE_API_BASE_URL=http://localhost:8000

CHANGELOG.md

@@ -0,0 +1,45 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+- **Project Management** - Create and manage projects with dashboard view
+- **Git Repository Management** - Bare repository initialization and mirror cloning with smart URL parsing
+- **Repository Workspace** - File browser with syntax highlighting, branch switching, and file editing
+- **Git History Visualization** - Commit history with graph visualization and diff viewing
+- **Git Control** - Branch management, commit, fetch/pull/push, merge operations
+- **File Editor** - Syntax highlighting for 50+ languages with edit/commit workflow
+- **Smart Git URL Parsing** - Automatic detection and correction of browser URLs to git clone URLs
+- **OAuth2 Authentication** - Session-based authentication via Authentik with simplified flow
+- **User Profile** - Profile management with avatar upload
+- **User Settings** - Theme selection, git identity, and preference management
+- **SSH Key Management** - Ed25519 key generation with secure storage
+- **Tool Types** - Built-in development tools (code-server, jupyter-notebook) with custom type support
+- **Comprehensive Documentation** - Architecture, API, deployment, and development guides
+
+### Changed
+
+- Simplified authentication from JWT to session-based cookies
+- Restructured test infrastructure with unit/integration/system separation
+- Improved Docker deployment with Traefik integration
+
+### Fixed
+
+- Database migration chain errors
+- Cross-origin cookie handling for OAuth flow
+- Nginx permission issues in container
+
+## [0.1.0] - 2026-05-19
+
+### Added
+
+- Initial release with core project and repository management
+- OAuth2 authentication with Authentik
+- Basic file browsing and git history viewing
+- Development tool type definitions

README.md

@@ -1,53 +1,195 @@
+# Headquarter
 
-## Testing Strategy
+A self-hosted platform for managing projects, git repositories, and development tools with OAuth2 authentication.
 
-The project uses a three-tier testing approach:
+## Overview
 
-### Test Categories
+Headquarter provides a centralized workspace for development teams to:
+- Manage projects and their associated git repositories
+- Browse repository files and view git history
+- Spawn development tools (VS Code Server, Jupyter Notebook, etc.)
+- Manage SSH keys and user preferences
 
-1. **Unit Tests** (`apps/api/tests/unit/`)
-   - Fast tests with no external dependencies
-   - Use SQLite in-memory database
-   - Run with: `make test-unit` or `pytest -m unit`
+## Features
 
-2. **Integration Tests** (`apps/api/tests/integration/`)
-   - Test API endpoints with database
-   - Use PostgreSQL with transaction rollback
-   - Run with: `make test-integration` or `pytest -m integration`
+### Project Management
+- Create and manage projects
+- View all projects in a dashboard
+- Click any project to open its workspace
 
-3. **System/E2E Tests** (`e2e/`)
-   - End-to-end tests using Playwright
-   - Test full user journeys
-   - Run with: `make test-e2e`
+### Git Repository Management
+- Initialize bare repositories
+- Clone repositories (including mirror clones)
+- Smart URL parsing (converts browser URLs to git URLs)
+- View repository history and commit details
 
-### Running Tests
+### Repository Workspace
+- Browse files and directories
+- View file contents with syntax highlighting
+- Switch between branches
+- Quick file editing with automatic commits
 
-```bash
-# Run all tests (excludes system tests by default)
-make test
+### Git History Visualization
+- View commit history with branch graph
+- See commit details, statistics, and diffs
+- Filter by branch
 
-# Run specific categories
-make test-unit          # Fast unit tests only
-make test-integration   # Integration tests with DB
-make test-system        # Full stack tests
-make test-e2e          # Browser-based E2E tests
+### Authentication
+- OAuth2 via Authentik
+- Session-based authentication
+- User profile management
 
-# Inside Docker container
-docker compose exec api pytest -v -m unit
-docker compose exec api pytest -v -m integration
+### Tool Management
+- Built-in tool types (code-server, jupyter-notebook)
+- Create custom tool types with Docker Compose templates
+- Template validation
+
+### User Settings
+- Theme selection (system/light/dark)
+- Git identity configuration
+- Default editor preference
+
+### SSH Key Management
+- Generate Ed25519 key pairs
+- Copy public keys to clipboard
+- Delete keys
+
+## Quick Start
+
+### Prerequisites
+- Docker and Docker Compose
+- Git
+
+### Local Development
+
+1. **Clone the repository:**
+   ```bash
+   git clone <repository-url>
+   cd headquarter
+   ```
+
+2. **Set up environment:**
+   ```bash
+   cp .env.example .env
+   # Edit .env with your settings
+   ```
+
+3. **Start services:**
+   ```bash
+   docker compose up -d
+   ```
+
+4. **Access the application:**
+   - Frontend: http://localhost:5173
+   - API: http://localhost:8000
+   - API Docs: http://localhost:8000/docs
+
+### Production Deployment
+
+See [Deployment Guide](docs/deployment/) for production setup with Traefik and Authentik.
+
+## Tech Stack
+
+### Backend
+- **FastAPI** - Python web framework
+- **SQLAlchemy** - ORM with async PostgreSQL support
+- **Pydantic** - Data validation
+- **Alembic** - Database migrations
+- **python-jose** - JWT handling
+
+### Frontend
+- **React** - UI library
+- **TypeScript** - Type safety
+- **Vite** - Build tool
+- **React Router** - Client-side routing
+
+### Infrastructure
+- **Docker** - Containerization
+- **PostgreSQL** - Database
+- **Traefik** - Reverse proxy (production)
+- **Authentik** - Identity provider
+
+## Documentation
+
+- [User Guide](docs/features/) - Feature documentation
+- [API Reference](docs/api/) - API endpoints
+- [Architecture](docs/architecture/) - System design
+- [Deployment](docs/deployment/) - Setup guides
+- [Development](docs/development/) - Contributing
+
+## Project Structure
+
+```
+.
+├── apps/
+│   ├── api/              # FastAPI backend
+│   │   ├── src/
+│   │   │   ├── api/      # API routes
+│   │   │   ├── auth/     # Authentication
+│   │   │   ├── models/   # Database models
+│   │   │   └── utils/    # Utilities
+│   │   ├── tests/        # Test suite
+│   │   └── Dockerfile
+│   └── web/              # React frontend
+│       ├── src/
+│       │   ├── api/      # API clients
+│       │   ├── components/# UI components
+│       │   └── pages/    # Page components
+│       └── Dockerfile
+├── docs/                 # Documentation
+├── docker-compose.yml    # Development setup
+├── docker-compose.traefik.yml  # Production setup
+└── Makefile             # Common commands
 ```
 
-### Test Markers
+## Development
 
-Tests are marked with pytest markers:
-- `@pytest.mark.unit` - Fast, isolated tests
-- `@pytest.mark.integration` - Tests with database/external services
-- `@pytest.mark.system` - Full stack tests
+### Backend Development
+```bash
+cd apps/api
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+uvicorn src.main:app --reload
+```
 
-### Shared Fixtures
+### Frontend Development
+```bash
+cd apps/web
+npm install
+npm run dev
+```
 
-Common fixtures are in `apps/api/tests/conftest.py`:
-- `sqlite_engine` - SQLite engine for unit tests
-- `postgres_engine` - PostgreSQL engine for integration tests
-- `db_session` - Database session with transaction rollback
-- `test_client` - FastAPI TestClient instance
+### Running Tests
+```bash
+# Backend tests
+make test
+
+# Frontend tests
+make test-web
+
+# All quality gates
+make lint
+make typecheck
+```
+
+## Configuration
+
+Key environment variables:
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `API_DOMAIN` | API domain | `localhost` |
+| `WEB_DOMAIN` | Web domain | `localhost` |
+| `AUTHENTIK_DOMAIN` | Authentik domain | - |
+| `AUTHENTIK_CLIENT_ID` | OAuth client ID | - |
+| `AUTHENTIK_CLIENT_SECRET` | OAuth client secret | - |
+| `DATABASE_URL` | PostgreSQL URL | - |
+| `JWT_SECRET` | JWT signing secret | - |
+| `REPO_BASE_PATH` | Repository storage path | `/data/repos` |
+
+See [Environment Variables](docs/deployment/environment.md) for complete list.
+
+## License
+
+[License information]

apps/api/Dockerfile

@@ -16,34 +16,50 @@ RUN pip install --no-cache-dir --user -e ".[dev]"
 # Production stage
 FROM python:3.11-slim
 
-# Create non-root user
-RUN groupadd -r appgroup && useradd -r -g appgroup appuser
+# Create non-root user and add to docker group
+RUN groupadd -r appgroup && useradd -r -g appgroup appuser \
+    && groupadd -r docker || true \
+    && usermod -aG docker appuser
 
 WORKDIR /app
 
-# Install runtime dependencies
+# Install runtime dependencies including Docker CLI
 RUN apt-get update && apt-get install -y --no-install-recommends \
     libpq5 \
     git \
     netcat-openbsd \
+    ca-certificates \
+    curl \
+    gnupg \
+    && install -m 0755 -d /etc/apt/keyrings \
+    && curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg \
+    && chmod a+r /etc/apt/keyrings/docker.gpg \
+    && echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian \
+    "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" > /etc/apt/sources.list.d/docker.list \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends docker-ce-cli docker-compose-plugin \
+    && curl -L --output /usr/local/bin/cloudflared https://github.com/cloudflare/cloudflared/releases/latest/download/cloudflared-linux-amd64 \
+    && chmod +x /usr/local/bin/cloudflared \
     && rm -rf /var/lib/apt/lists/*
 
 # Copy dependencies from builder
-COPY --from=builder /root/.local /home/appuser/.local
-ENV PATH=/home/appuser/.local/bin:$PATH
+COPY --from=builder /root/.local /root/.local
+ENV PATH=/root/.local/bin:$PATH
 
 # Copy application code
 COPY --chown=appuser:appgroup . .
 
-# Create directories for repo storage
-RUN mkdir -p /data/repos && chown -R appuser:appgroup /data/repos
+# Create directories for repo and instance storage
+RUN mkdir -p /data/repos /data/instances && chown -R appuser:appgroup /data
 
 # Copy wait-for-db script
 COPY wait-for-db.sh /usr/local/bin/wait-for-db.sh
 RUN chmod +x /usr/local/bin/wait-for-db.sh
 
-# Switch to non-root user
-USER appuser
+# NOTE: Running as root to access Docker socket for managing tool instances
+# This is required because Docker socket permissions require root or docker group membership
+# which doesn't work well across container boundaries.
+# Consider using Docker-in-Docker or rootless Docker for production hardening.
 
 # Expose port
 EXPOSE 8000

apps/api/README.md

@@ -0,0 +1,252 @@
+# Headquarter API
+
+The backend API for Headquarter - a self-hosted platform for managing projects, git repositories, and development tools.
+
+## Overview
+
+Built with **FastAPI** and **SQLAlchemy** (async), using **PostgreSQL** for data storage and **Docker** for tool instance management.
+
+### Tech Stack
+
+- **Framework**: FastAPI (Python 3.12+)
+- **Database**: PostgreSQL 15+ with asyncpg
+- **ORM**: SQLAlchemy 2.0 (async)
+- **Auth**: OAuth2 via Authentik with session cookies
+- **Migrations**: Alembic
+- **Tools**: Docker Compose for instance management
+
+## Quick Start
+
+### Prerequisites
+
+- Python 3.12+
+- PostgreSQL 15+ running locally
+- Docker (for tool instances)
+
+### Setup
+
+```bash
+cd apps/api
+
+# Create virtual environment
+python -m venv .venv
+source .venv/bin/activate
+
+# Install dependencies
+pip install -e ".[dev]"
+
+# Set up database
+# Ensure PostgreSQL is running with a 'headquarter' database
+
+# Run migrations
+alembic upgrade head
+
+# Start development server
+uvicorn src.main:app --reload --port 8000
+```
+
+The API will be available at `http://localhost:8000`.
+
+### Interactive Documentation
+
+Once running, visit:
+- **Swagger UI**: http://localhost:8000/docs
+- **ReDoc**: http://localhost:8000/redoc
+- **OpenAPI JSON**: http://localhost:8000/openapi.json
+
+## Environment Variables
+
+| Variable | Required | Default | Description |
+|----------|----------|---------|-------------|
+| `DATABASE_URL` | Yes | - | PostgreSQL connection string |
+| `API_BASE_URL` | Yes | - | Public API URL (e.g., `https://api.example.com`) |
+| `AUTHENTIK_DOMAIN` | Yes | - | Authentik server domain |
+| `AUTHENTIK_CLIENT_ID` | Yes | - | OAuth2 client ID |
+| `AUTHENTIK_CLIENT_SECRET` | Yes | - | OAuth2 client secret |
+| `AUTHENTIK_APPLICATION_SLUG` | Yes | - | Authentik application slug |
+| `WEB_BASE_URL` | Yes | - | Public frontend URL |
+| `SESSION_SECRET` | Yes | - | Secret for session cookie signing |
+| `COOKIE_DOMAIN` | No | - | Cookie domain (e.g., `.example.com`) |
+| `UPLOAD_DIR` | No | `./uploads` | Directory for file uploads |
+| `REPO_BASE_PATH` | No | `./repositories` | Base path for git repositories |
+| `INSTANCES_BASE_PATH` | No | `./instances` | Base path for tool instances |
+| `LOG_LEVEL` | No | `INFO` | Logging level |
+
+## Development
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run specific test category
+pytest -m unit          # Unit tests (no DB)
+pytest -m integration   # Integration tests (requires DB)
+
+# Run with coverage
+pytest --cov=src --cov-report=html
+```
+
+### Code Quality
+
+```bash
+# Format code
+ruff format src tests
+
+# Lint
+ruff check src tests
+
+# Type check
+mypy src
+```
+
+### Database Migrations
+
+```bash
+# Create new migration
+alembic revision --autogenerate -m "description"
+
+# Apply migrations
+alembic upgrade head
+
+# Rollback one migration
+alembic downgrade -1
+
+# Show current revision
+alembic current
+```
+
+## Architecture
+
+### Directory Structure
+
+```
+src/
+├── api/              # API endpoint routers
+│   ├── auth.py       # OAuth2 authentication
+│   ├── dashboard.py  # Dashboard summary
+│   ├── git_repositories.py  # Git repo management
+│   ├── health.py     # Health checks
+│   ├── projects.py   # Project CRUD
+│   ├── ssh_keys.py   # SSH key management
+│   ├── terminal.py   # WebSocket terminal
+│   ├── tool_instances.py  # Tool instance management
+│   ├── tool_types.py # Tool type definitions
+│   ├── user_config.py # User preferences
+│   └── users.py      # User profile
+├── auth/             # Authentication logic
+│   ├── cookies.py    # Cookie utilities
+│   ├── dependencies.py # Auth dependencies
+│   ├── oidc.py       # OpenID Connect
+│   └── session.py    # Session management
+├── config.py         # Application settings
+├── database.py       # Database setup
+├── main.py           # FastAPI application
+├── models/           # SQLAlchemy models
+├── schemas/          # Pydantic schemas
+├── services/         # Business logic
+│   ├── docker.py     # Docker Compose management
+│   ├── terminal_manager.py  # Terminal sessions
+│   └── terminal_session.py  # Terminal I/O
+└── utils/            # Utilities
+    ├── git_control.py      # Git operations
+    ├── git_files.py        # File operations
+    ├── git_history.py      # History extraction
+    └── git_url_parser.py   # URL parsing
+```
+
+### Authentication Flow
+
+1. User clicks "Login" → redirects to Authentik OAuth
+2. Authentik redirects back with authorization code
+3. API exchanges code for tokens and fetches user info
+4. API creates session cookie (HMAC-signed, httpOnly)
+5. Frontend stores nothing - cookie sent automatically
+6. Subsequent requests include cookie for authentication
+
+### Data Flow
+
+```
+Client → FastAPI Router → Auth Dependency → Service Layer → Database
+                ↓
+         Pydantic Models (validation)
+                ↓
+         SQLAlchemy Models (ORM)
+                ↓
+         PostgreSQL (storage)
+```
+
+## API Endpoints
+
+### Authentication
+- `GET /auth/login` - Initiate OAuth login
+- `GET /auth/callback` - OAuth callback
+- `GET /auth/me` - Get current user
+- `POST /auth/logout` - Logout
+
+### Projects
+- `GET /projects` - List projects
+- `POST /projects` - Create project
+- `GET /projects/{id}` - Get project
+- `PUT /projects/{id}` - Update project
+- `DELETE /projects/{id}` - Delete project
+
+### Git Repositories
+- `GET /projects/{id}/repositories` - List repositories
+- `POST /projects/{id}/repositories` - Create repository
+- `GET /projects/{id}/repositories/{id}` - Get repository
+- `DELETE /projects/{id}/repositories/{id}` - Delete repository
+- `GET /projects/{id}/repositories/{id}/files` - List files
+- `GET /projects/{id}/repositories/{id}/files/content` - Get file content
+- `POST /projects/{id}/repositories/{id}/files/content` - Update file
+- `GET /projects/{id}/repositories/{id}/branches` - List branches
+- `GET /projects/{id}/repositories/{id}/history` - Commit history
+- `GET /projects/{id}/repositories/{id}/commits/{hash}` - Commit detail
+
+### Tool Types
+- `GET /tool-types` - List tool types
+- `POST /tool-types` - Create tool type
+- `GET /tool-types/{id}` - Get tool type
+- `PUT /tool-types/{id}` - Update tool type
+- `DELETE /tool-types/{id}` - Delete tool type
+
+### Tool Instances
+- `GET /tool-instances` - List instances
+- `POST /tool-instances` - Create instance
+- `GET /tool-instances/{id}` - Get instance
+- `POST /tool-instances/{id}/start` - Start instance
+- `POST /tool-instances/{id}/stop` - Stop instance
+- `POST /tool-instances/{id}/restart` - Restart instance
+- `DELETE /tool-instances/{id}` - Delete instance
+- `GET /tool-instances/{id}/logs` - Get logs
+
+### Terminal
+- `WS /ws/tool-instances/{id}/terminal` - WebSocket terminal
+
+### Users
+- `GET /users/me` - Get profile
+- `PUT /users/me` - Update profile
+- `POST /users/me/avatar` - Upload avatar
+- `GET /users/me/config` - Get config
+- `PATCH /users/me/config` - Update config
+
+### SSH Keys
+- `GET /ssh-keys` - List keys
+- `POST /ssh-keys` - Create key
+- `DELETE /ssh-keys/{id}` - Delete key
+
+### Health
+- `GET /health` - System health
+- `GET /health/db` - Database health
+
+## Deployment
+
+See the [deployment documentation](../../docs/deployment/) for Docker and Traefik setup.
+
+## Contributing
+
+1. Follow PEP 8 style guide
+2. Add tests for new endpoints
+3. Update documentation
+4. Run quality gates before committing

apps/api/alembic/versions/0003_user_configs.py

@@ -27,7 +27,8 @@ def upgrade() -> None:
         sa.Column('updated_at', sa.DateTime(timezone=True), server_default=sa.text('now()'), nullable=False),
         sa.ForeignKeyConstraint(['user_id'], ['users.id'], ),
         sa.PrimaryKeyConstraint('id'),
-        sa.UniqueConstraint('user_id')
+        sa.UniqueConstraint('user_id'),
+        if_not_exists=True,
     )
 
 

apps/api/alembic/versions/0004_tool_types.py

@@ -42,6 +42,7 @@ def upgrade() -> None:
             onupdate=sa.text("now()"),
             nullable=False,
         ),
+        if_not_exists=True,
     )
 
 

apps/api/alembic/versions/0005_ssh_keys_timestamps.py

@@ -0,0 +1,44 @@
+"""add timestamps to ssh_keys table
+
+Revision ID: 0005_ssh_keys_timestamps
+Revises: 0004_tool_types
+Create Date: 2026-05-19 09:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "0005_ssh_keys_timestamps"
+down_revision: Union[str, None] = "0004_tool_types"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "ssh_keys",
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=True,
+        ),
+    )
+    op.add_column(
+        "ssh_keys",
+        sa.Column(
+            "updated_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=True,
+        ),
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("ssh_keys", "updated_at")
+    op.drop_column("ssh_keys", "created_at")

apps/api/alembic/versions/0006_tool_instances.py

@@ -0,0 +1,55 @@
+"""add tool_instances table
+
+Revision ID: 0006_tool_instances
+Revises: 0005_ssh_keys_timestamps
+Create Date: 2026-05-19 10:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0006_tool_instances"
+down_revision: Union[str, None] = "0005_ssh_keys_timestamps"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "tool_instances",
+        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
+        sa.Column("name", sa.String(255), nullable=False),
+        sa.Column("display_name", sa.String(255), nullable=False),
+        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("repository_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("owner_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("status", sa.String(50), nullable=False, server_default="pending"),
+        sa.Column("container_id", sa.String(255), nullable=True),
+        sa.Column("compose_path", sa.String(1024), nullable=True),
+        sa.Column("url", sa.String(1024), nullable=True),
+        sa.Column("port", sa.Integer(), nullable=True),
+        sa.Column("last_started_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("last_stopped_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.ForeignKeyConstraint(["tool_type_id"], ["tool_types.id"]),
+        sa.ForeignKeyConstraint(["repository_id"], ["git_repositories.id"]),
+        sa.ForeignKeyConstraint(["project_id"], ["projects.id"]),
+        sa.ForeignKeyConstraint(["owner_id"], ["users.id"]),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_tool_instances_owner", "tool_instances", ["owner_id"])
+    op.create_index("idx_tool_instances_repo", "tool_instances", ["repository_id"])
+    op.create_index("idx_tool_instances_status", "tool_instances", ["status"])
+
+
+def downgrade() -> None:
+    op.drop_index("idx_tool_instances_status", table_name="tool_instances")
+    op.drop_index("idx_tool_instances_repo", table_name="tool_instances")
+    op.drop_index("idx_tool_instances_owner", table_name="tool_instances")
+    op.drop_table("tool_instances")

apps/api/alembic/versions/0007_instance_container_name.py

@@ -0,0 +1,28 @@
+"""add container_name to tool_instances
+
+Revision ID: 0007_instance_container_name
+Revises: 0006_tool_instances
+Create Date: 2026-05-20 08:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0007_instance_container_name"
+down_revision: Union[str, None] = "0006_tool_instances"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_instances",
+        sa.Column("container_name", sa.String(255), nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_instances", "container_name")

apps/api/alembic/versions/0008_tool_type_category.py

@@ -0,0 +1,33 @@
+"""add category and interfaces to tool_types
+
+Revision ID: 0008_tool_type_category
+Revises: 0007_instance_container_name
+Create Date: 2026-05-20 09:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0008_tool_type_category"
+down_revision: Union[str, None] = "0007_instance_container_name"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_types",
+        sa.Column("category", sa.String(50), nullable=False, server_default="other")
+    )
+    op.add_column(
+        "tool_types",
+        sa.Column("interfaces", sa.JSON(), nullable=False, server_default='["web"]')
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_types", "interfaces")
+    op.drop_column("tool_types", "category")

apps/api/alembic/versions/0009_tool_configs.py

@@ -0,0 +1,46 @@
+"""add tool_configs table
+
+Revision ID: 0009_tool_configs
+Revises: 0008_tool_type_category
+Create Date: 2026-05-20 09:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0009_tool_configs"
+down_revision: Union[str, None] = "0008_tool_type_category"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "tool_configs",
+        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
+        sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+        sa.Column("key", sa.String(255), nullable=False),
+        sa.Column("value", sa.Text(), nullable=False),
+        sa.Column("config_type", sa.String(20), nullable=False, server_default="env"),
+        sa.Column("file_path", sa.String(1024), nullable=True),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.ForeignKeyConstraint(["user_id"], ["users.id"]),
+        sa.ForeignKeyConstraint(["tool_type_id"], ["tool_types.id"]),
+        sa.ForeignKeyConstraint(["project_id"], ["projects.id"]),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_tool_configs_user_tool", "tool_configs", ["user_id", "tool_type_id"])
+    op.create_index("idx_tool_configs_project", "tool_configs", ["project_id"])
+
+
+def downgrade() -> None:
+    op.drop_index("idx_tool_configs_project", table_name="tool_configs")
+    op.drop_index("idx_tool_configs_user_tool", table_name="tool_configs")
+    op.drop_table("tool_configs")

apps/api/alembic/versions/0010_tool_type_default_port.py

@@ -0,0 +1,28 @@
+"""add default_port to tool_types
+
+Revision ID: 0010_tool_type_default_port
+Revises: 0009_tool_configs
+Create Date: 2026-05-20 10:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0010_tool_type_default_port"
+down_revision: Union[str, None] = "0009_tool_configs"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_types",
+        sa.Column("default_port", sa.Integer(), nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_types", "default_port")

apps/api/alembic/versions/0011_tool_instance_tunnel_fields.py

@@ -0,0 +1,33 @@
+"""add tunnel fields to tool_instances
+
+Revision ID: 0011_tool_instance_tunnel_fields
+Revises: 0010_tool_type_default_port
+Create Date: 2026-05-20 12:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0011_tool_instance_tunnel_fields"
+down_revision: Union[str, None] = "0010_tool_type_default_port"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_instances",
+        sa.Column("public_url", sa.String(1024), nullable=True)
+    )
+    op.add_column(
+        "tool_instances",
+        sa.Column("tunnel_id", sa.String(255), nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_instances", "tunnel_id")
+    op.drop_column("tool_instances", "public_url")

apps/api/alembic/versions/0012_default_port_req.py

@@ -0,0 +1,48 @@
+"""make default_port non-nullable and set values
+
+Revision ID: 0012_default_port_req
+Revises: 0011_tool_instance_tunnel_fields
+Create Date: 2026-05-20 15:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0012_default_port_req"
+down_revision: Union[str, None] = "0011_tool_instance_tunnel_fields"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Set default_port for existing built-in tool types
+    op.execute("""
+        UPDATE tool_types 
+        SET default_port = CASE 
+            WHEN name = 'code-server' THEN 8443
+            WHEN name = 'jupyter-notebook' THEN 8888
+            WHEN name = 'opencode' THEN 3000
+            ELSE 8080
+        END
+        WHERE default_port IS NULL
+    """)
+    
+    # Make default_port non-nullable
+    op.alter_column(
+        "tool_types",
+        "default_port",
+        existing_type=sa.Integer(),
+        nullable=False,
+    )
+
+
+def downgrade() -> None:
+    op.alter_column(
+        "tool_types",
+        "default_port",
+        existing_type=sa.Integer(),
+        nullable=True,
+    )

apps/api/alembic/versions/0013_add_config_profiles.py

@@ -0,0 +1,104 @@
+"""add config profiles, includes, mounts, and tool instance profile selection
+
+Revision ID: 0013_add_config_profiles
+Revises: 0012_default_port_req
+Create Date: 2026-05-24 12:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0013_add_config_profiles"
+down_revision: Union[str, None] = "0012_default_port_req"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Create config_profiles table
+    op.create_table(
+        "config_profiles",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("name", sa.String(length=255), nullable=False),
+        sa.Column("description", sa.Text(), nullable=True),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
+    op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+
+    # Create config_includes table
+    op.create_table(
+        "config_includes",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("included_profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.ForeignKeyConstraint(["profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["included_profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("profile_id", "included_profile_id", name="uq_config_includes_pair"),
+    )
+    op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
+    op.create_index("idx_config_includes_included", "config_includes", ["included_profile_id"])
+
+    # Create config_mounts table
+    op.create_table(
+        "config_mounts",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("mount_path", sa.String(length=1024), nullable=False),
+        sa.Column("content", sa.Text(), nullable=True),
+        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.ForeignKeyConstraint(["profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
+
+    # Add selected_profile_id to tool_instances
+    op.add_column(
+        "tool_instances",
+        sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.create_foreign_key(
+        "fk_tool_instances_selected_profile",
+        "tool_instances",
+        "config_profiles",
+        ["selected_profile_id"],
+        ["id"],
+        ondelete="SET NULL",
+    )
+    op.create_index("idx_tool_instances_selected_profile", "tool_instances", ["selected_profile_id"])
+
+
+def downgrade() -> None:
+    # Remove selected_profile_id from tool_instances
+    op.drop_index("idx_tool_instances_selected_profile", table_name="tool_instances")
+    op.drop_constraint("fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey")
+    op.drop_column("tool_instances", "selected_profile_id")
+
+    # Drop config_mounts
+    op.drop_index("idx_config_mounts_profile", table_name="config_mounts")
+    op.drop_table("config_mounts")
+
+    # Drop config_includes
+    op.drop_index("idx_config_includes_included", table_name="config_includes")
+    op.drop_index("idx_config_includes_profile", table_name="config_includes")
+    op.drop_table("config_includes")
+
+    # Drop config_profiles
+    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
+    op.drop_table("config_profiles")

apps/api/alembic/versions/398082499c30_add_tool_config_fields.py

@@ -0,0 +1,40 @@
+"""add_tool_config_fields
+
+Revision ID: 398082499c30
+Revises: af8512103d67
+Create Date: 2026-05-22 18:38:20.166184
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '398082499c30'
+down_revision = 'af8512103d67'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # Add new columns to tool_configs
+    op.add_column('tool_configs', sa.Column('port_override', sa.Integer(), nullable=True))
+    op.add_column('tool_configs', sa.Column('start_command', sa.Text(), nullable=True))
+    op.add_column('tool_configs', sa.Column('working_directory', sa.Text(), nullable=True))
+    op.add_column('tool_configs', sa.Column('environment_variables', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='{}'))
+    op.add_column('tool_configs', sa.Column('volumes', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='[]'))
+    
+    # Add CHECK constraint for port range
+    op.create_check_constraint('chk_port_range', 'tool_configs', sa.text('port_override IS NULL OR (port_override >= 1 AND port_override <= 65535)'))
+
+
+def downgrade() -> None:
+    # Drop CHECK constraint
+    op.drop_constraint('chk_port_range', 'tool_configs', type_='check')
+    
+    # Drop columns
+    op.drop_column('tool_configs', 'port_override')
+    op.drop_column('tool_configs', 'start_command')
+    op.drop_column('tool_configs', 'working_directory')
+    op.drop_column('tool_configs', 'environment_variables')
+    op.drop_column('tool_configs', 'volumes')

apps/api/alembic/versions/8ed7dd80973d_create_config_folders_table.py

@@ -0,0 +1,44 @@
+"""create_config_folders_table
+
+Revision ID: 8ed7dd80973d
+Revises: 398082499c30
+Create Date: 2026-05-22 18:38:22.133696
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '8ed7dd80973d'
+down_revision = '398082499c30'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        'config_folders',
+        sa.Column('id', postgresql.UUID(as_uuid=True), primary_key=True, server_default=sa.text('gen_random_uuid()')),
+        sa.Column('user_id', postgresql.UUID(as_uuid=True), sa.ForeignKey('users.id', ondelete='CASCADE'), nullable=False),
+        sa.Column('name', sa.String(255), nullable=False),
+        sa.Column('description', sa.Text(), nullable=True),
+        sa.Column('mount_path', sa.String(1024), nullable=False),
+        sa.Column('files', postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default='{}'),
+        sa.Column('project_overrides', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='{}'),
+        sa.Column('is_active', sa.Boolean(), nullable=False, server_default='true'),
+        sa.Column('created_at', sa.DateTime(timezone=True), nullable=False, server_default=sa.text('NOW()')),
+        sa.Column('updated_at', sa.DateTime(timezone=True), nullable=False, server_default=sa.text('NOW()')),
+        sa.UniqueConstraint('user_id', 'name', name='uq_config_folders_user_name')
+    )
+    
+    # Add index on user_id for filtering
+    op.create_index('idx_config_folders_user', 'config_folders', ['user_id'])
+
+
+def downgrade() -> None:
+    # Drop index
+    op.drop_index('idx_config_folders_user', table_name='config_folders')
+    
+    # Drop table
+    op.drop_table('config_folders')

apps/api/alembic/versions/af8512103d67_add_tool_type_fields.py

@@ -0,0 +1,38 @@
+"""add_tool_type_fields
+
+Revision ID: af8512103d67
+Revises: 0012_default_port_req
+Create Date: 2026-05-22 18:37:56.607240
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = 'af8512103d67'
+down_revision = '0012_default_port_req'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # Add new columns to tool_types
+    op.add_column('tool_types', sa.Column('definition_type', sa.String(20), nullable=False, server_default='compose'))
+    op.add_column('tool_types', sa.Column('dockerfile_template', sa.Text(), nullable=True))
+    op.add_column('tool_types', sa.Column('build_context', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='{}'))
+    op.add_column('tool_types', sa.Column('readiness_probe', postgresql.JSONB(astext_type=sa.Text()), nullable=True))
+    
+    # Add CHECK constraint for definition_type
+    op.create_check_constraint('chk_definition_type', 'tool_types', sa.text("definition_type IN ('compose', 'dockerfile')"))
+
+
+def downgrade() -> None:
+    # Drop CHECK constraint
+    op.drop_constraint('chk_definition_type', 'tool_types', type_='check')
+    
+    # Drop columns
+    op.drop_column('tool_types', 'definition_type')
+    op.drop_column('tool_types', 'dockerfile_template')
+    op.drop_column('tool_types', 'build_context')
+    op.drop_column('tool_types', 'readiness_probe')

apps/api/pyproject.toml

@@ -11,7 +11,6 @@ dependencies = [
     "alembic>=1.12.0",
     "pydantic>=2.5.0",
     "pydantic-settings>=2.1.0",
-    "python-jose[cryptography]>=3.3.0",
     "python-multipart>=0.0.6",
     "httpx>=0.25.0",
     "structlog>=23.2.0",

apps/api/src/api/auth.py

@@ -1,7 +1,6 @@
 import logging
 from secrets import token_urlsafe
-from datetime import UTC, datetime, timedelta
-from typing import AsyncGenerator, Literal, cast
+from typing import Any, AsyncGenerator, Literal, cast
 
 import httpx
 from fastapi import APIRouter, Cookie, Depends, HTTPException, Response, status
@@ -10,14 +9,8 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.cookies import build_cookie_options
-from src.auth.jwt_service import decode_access_token, mint_access_token
-from src.auth.oidc import (
-    build_login_redirect_url,
-    exchange_code_for_tokens,
-    fetch_jwks,
-    verify_provider_access_token,
-)
-from src.auth.refresh_store import create_refresh_token, revoke_refresh_token, rotate_refresh_token
+from src.auth.oidc import build_login_redirect_url, exchange_code_for_tokens, fetch_user_info
+from src.auth.session import create_session_cookie, decode_session_cookie
 from src.config import Settings
 from src.database import SessionLocal
 from src.models.user import User
@@ -32,8 +25,21 @@ async def get_db_session() -> AsyncGenerator[AsyncSession, None]:
         yield session
 
 
-@router.get("/login")
-async def login() -> RedirectResponse:
+@router.get(
+    "/login",
+    summary="Initiate OAuth login",
+    description="Redirects to the configured OAuth provider (Authentik) to start the authentication flow.",
+    response_class=RedirectResponse,
+)
+async def login(next: str = "/") -> RedirectResponse:
+    """Initiate OAuth2 login flow.
+
+    Args:
+        next: URL to redirect to after successful authentication.
+
+    Returns:
+        RedirectResponse to the OAuth provider's authorization endpoint.
+    """
     settings = Settings()
     redirect_uri = f"{settings.api_base_url}/auth/callback"
     state = token_urlsafe(24)
@@ -41,11 +47,11 @@ async def login() -> RedirectResponse:
         settings=settings,
         redirect_uri=redirect_uri,
         state=state,
-        nonce=token_urlsafe(16),
     )
-    logger.info("Auth login initiated: redirect_uri=%s", redirect_uri)
+    logger.info("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
     response = RedirectResponse(location)
     response.set_cookie("auth_state", state, httponly=True, samesite="lax")
+    response.set_cookie("auth_next", next, httponly=True, samesite="lax")
     return response
 
 
@@ -53,10 +59,10 @@ async def login() -> RedirectResponse:
 async def callback(
     code: str,
     state: str,
-    response: Response,
     auth_state: str | None = Cookie(default=None),
+    auth_next: str | None = Cookie(default="/"),
     session: AsyncSession = Depends(get_db_session),
-) -> dict[str, str]:
+) -> RedirectResponse:
     logger.info("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
     
     if auth_state is None or auth_state != state:
@@ -75,32 +81,25 @@ async def callback(
                 redirect_uri=redirect_uri,
                 client=client,
             )
-            logger.info("Token exchange successful: access_token=%s...", token_payload["access_token"][:20] if token_payload.get("access_token") else "None")
+            logger.info("Token exchange successful")
         except Exception as exc:
             logger.error("Token exchange failed: %s", exc)
             raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"token exchange failed: {exc}")
         
         try:
-            jwks = await fetch_jwks(settings=settings, client=client)
-            logger.info("JWKS fetched successfully")
+            user_info = await fetch_user_info(
+                settings=settings,
+                access_token=token_payload["access_token"],
+                client=client,
+            )
+            logger.info("User info fetched successfully")
         except Exception as exc:
-            logger.error("JWKS fetch failed: %s", exc)
-            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="failed to fetch JWKS")
+            logger.error("User info fetch failed: %s", exc)
+            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="failed to fetch user info")
 
-    try:
-        provider_claims = verify_provider_access_token(
-            settings=settings,
-            token=token_payload["access_token"],
-            jwks=jwks,
-        )
-        logger.info("Token verified successfully for sub=%s", provider_claims.get("sub"))
-    except Exception as exc:
-        logger.error("Token verification failed: %s", exc)
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid token")
-
-    authentik_id = str(provider_claims["sub"])
-    email = str(provider_claims.get("email", f"{authentik_id}@authentik.local"))
-    name = str(provider_claims.get("name", email))
+    authentik_id = str(user_info.get("sub", ""))
+    email = str(user_info.get("email", f"{authentik_id}@authentik.local"))
+    name = str(user_info.get("name", email))
     logger.info("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
 
     try:
@@ -121,109 +120,80 @@ async def callback(
         logger.error("Database error during user lookup/creation: %s", exc)
         raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="database error")
 
-    try:
-        access_token = mint_access_token(
-            settings=settings,
-            subject=str(user.id),
-            email=user.email,
-            name=user.name,
-            expires_at=datetime.now(UTC) + timedelta(minutes=settings.access_token_ttl_minutes),
-        )
-        refresh_token, _ = await create_refresh_token(
-            session=session,
-            user_id=user.id,
-            expires_at=datetime.now(UTC) + timedelta(days=settings.refresh_token_ttl_days),
-            user_agent=None,
-            ip_address=None,
-        )
-        logger.info("Tokens created for user id=%s", user.id)
-    except Exception as exc:
-        logger.error("Token creation failed: %s", exc)
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="token creation failed")
-
+    # Create session cookie
+    session_cookie = create_session_cookie(settings=settings, user_id=str(user.id))
+    
     cookie_options = build_cookie_options(settings)
     cookie_samesite = cast(Literal["lax", "strict", "none"], cookie_options["samesite"])
     cookie_secure = bool(cookie_options["secure"])
-    response.set_cookie("access_token", access_token, httponly=True, samesite=cookie_samesite, secure=cookie_secure)
-    response.set_cookie("refresh_token", refresh_token, httponly=True, samesite=cookie_samesite, secure=cookie_secure)
-    response.delete_cookie("auth_state", samesite="lax")
-
-    logger.info("Auth callback complete for user id=%s", user.id)
-    return {"sub": str(user.id), "email": user.email, "name": user.name}
-
-
-@router.post("/refresh")
-async def refresh(
-    response: Response,
-    refresh_token: str | None = Cookie(default=None),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict[str, str]:
-    if not refresh_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing refresh token")
-
-    settings = Settings()
-    try:
-        rotated_raw_token, rotated_record = await rotate_refresh_token(
-            session=session,
-            raw_token=refresh_token,
-            user_agent=None,
-            ip_address=None,
-        )
-    except ValueError as error:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=str(error)) from error
-
-    user = await session.get(User, rotated_record.user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid refresh token")
-
-    access_token = mint_access_token(
-        settings=settings,
-        subject=str(user.id),
-        email=user.email,
-        name=user.name,
-        expires_at=datetime.now(UTC) + timedelta(minutes=settings.access_token_ttl_minutes),
+    cookie_domain = str(cookie_options["domain"]) if cookie_options.get("domain") else None
+    
+    logger.info("Auth callback complete for user id=%s, redirecting to %s", user.id, auth_next)
+    
+    # Redirect to frontend with the original next path
+    redirect_url = f"{settings.web_base_url}{auth_next}"
+    redirect_response = RedirectResponse(url=redirect_url)
+    
+    redirect_response.set_cookie(
+        "session", 
+        session_cookie, 
+        httponly=True, 
+        samesite=cookie_samesite, 
+        secure=cookie_secure,
+        domain=cookie_domain,
     )
-
-    cookie_options = build_cookie_options(settings)
-    cookie_samesite = cast(Literal["lax", "strict", "none"], cookie_options["samesite"])
-    cookie_secure = bool(cookie_options["secure"])
-
-    response.set_cookie("access_token", access_token, httponly=True, samesite=cookie_samesite, secure=cookie_secure)
-    response.set_cookie("refresh_token", rotated_raw_token, httponly=True, samesite=cookie_samesite, secure=cookie_secure)
-
-    return {"sub": str(user.id), "email": user.email, "name": user.name}
+    redirect_response.delete_cookie("auth_state", samesite="lax", domain=cookie_domain)
+    redirect_response.delete_cookie("auth_next", samesite="lax", domain=cookie_domain)
+    
+    return redirect_response
 
 
 @router.post("/logout")
-async def logout(
-    response: Response,
-    refresh_token: str | None = Cookie(default=None),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict[str, str]:
+async def logout(response: Response) -> dict[str, str]:
     settings = Settings()
     cookie_options = build_cookie_options(settings)
     cookie_samesite = cast(Literal["lax", "strict", "none"], cookie_options["samesite"])
     cookie_secure = bool(cookie_options["secure"])
+    cookie_domain = str(cookie_options["domain"]) if cookie_options.get("domain") else None
 
-    if refresh_token:
-        try:
-            await revoke_refresh_token(session=session, raw_token=refresh_token)
-        except Exception:
-            pass
-
-    response.delete_cookie("access_token", samesite=cookie_samesite, secure=cookie_secure)
-    response.delete_cookie("refresh_token", samesite=cookie_samesite, secure=cookie_secure)
+    response.delete_cookie("session", samesite=cookie_samesite, secure=cookie_secure, domain=cookie_domain)
     return {"status": "ok"}
 
 
 @router.get("/me")
-async def me(access_token: str | None = Cookie(default=None)) -> dict[str, str]:
-    if not access_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing access token")
+async def me(
+    session_cookie: str | None = Cookie(default=None, alias="session"),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict[str, Any]:
+    logger.info("Auth /me called, cookie present: %s", bool(session_cookie))
+    
+    if not session_cookie:
+        logger.warning("Auth /me: missing session cookie")
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing session")
 
-    claims = decode_access_token(settings=Settings(), token=access_token)
+    settings = Settings()
+    logger.info("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
+                settings.cookie_domain, settings.cookie_secure, settings.cookie_samesite)
+    
+    try:
+        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+        user_id = payload["user_id"]
+        logger.info("Auth /me: decoded session for user_id=%s", user_id)
+    except ValueError as exc:
+        logger.warning("Auth /me: invalid session: %s", exc)
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc))
+
+    user = await session.get(User, user_id)
+    if user is None:
+        logger.warning("Auth /me: user not found for id=%s", user_id)
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
+
+    logger.info("Auth /me: success for user=%s", user.email)
     return {
-        "sub": str(claims["sub"]),
-        "email": str(claims["email"]),
-        "name": str(claims["name"]),
+        "user": {
+            "id": str(user.id),
+            "email": user.email,
+            "name": user.name,
+            "avatar_url": user.avatar_url or "",
+        }
     }

apps/api/src/api/config_folders.py

@@ -0,0 +1,372 @@
+"""Config folder API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from pydantic import BaseModel, Field, field_validator
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.config_folder import ConfigFolder
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-folders", tags=["config-folders"])
+
+MAX_FOLDER_SIZE_MB = 10
+MAX_FOLDER_SIZE_BYTES = MAX_FOLDER_SIZE_MB * 1024 * 1024
+
+
+class ConfigFolderCreate(BaseModel):
+    name: str = Field(description="Folder name (unique per user)")
+    description: str | None = Field(default=None, description="Optional description")
+    mount_path: str = Field(description="Default mount path in container")
+    files: dict = Field(default_factory=dict, description="Files as {path: content}")
+
+    @field_validator("mount_path")
+    @classmethod
+    def validate_mount_path(cls, v: str) -> str:
+        if not v.startswith("/"):
+            raise ValueError("Mount path must be absolute (start with /)")
+        return v
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        total_size = 0
+        for path, content in v.items():
+            # Check for path traversal
+            if ".." in path or path.startswith("/"):
+                raise ValueError(f"Invalid file path: {path}")
+            total_size += len(content.encode("utf-8"))
+        
+        if total_size > MAX_FOLDER_SIZE_BYTES:
+            raise ValueError(f"Total folder size exceeds {MAX_FOLDER_SIZE_MB}MB limit")
+        
+        return v
+
+
+class ConfigFolderUpdate(BaseModel):
+    name: str | None = Field(default=None, description="Folder name")
+    description: str | None = Field(default=None, description="Optional description")
+    mount_path: str | None = Field(default=None, description="Default mount path")
+    files: dict | None = Field(default=None, description="Files as {path: content}")
+    is_active: bool | None = Field(default=None, description="Active/inactive toggle")
+
+    @field_validator("mount_path")
+    @classmethod
+    def validate_mount_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if not v.startswith("/"):
+            raise ValueError("Mount path must be absolute (start with /)")
+        return v
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict | None) -> dict | None:
+        if v is None:
+            return v
+        
+        total_size = 0
+        for path, content in v.items():
+            # Check for path traversal
+            if ".." in path or path.startswith("/"):
+                raise ValueError(f"Invalid file path: {path}")
+            total_size += len(content.encode("utf-8"))
+        
+        if total_size > MAX_FOLDER_SIZE_BYTES:
+            raise ValueError(f"Total folder size exceeds {MAX_FOLDER_SIZE_MB}MB limit")
+        
+        return v
+
+
+class ProjectOverrideCreate(BaseModel):
+    mount_path: str | None = Field(default=None, description="Override mount path")
+    files: dict = Field(default_factory=dict, description="Override files")
+
+    @field_validator("mount_path")
+    @classmethod
+    def validate_mount_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if not v.startswith("/"):
+            raise ValueError("Mount path must be absolute (start with /)")
+        return v
+
+
+class ConfigFolderResponse(BaseModel):
+    id: str
+    user_id: str
+    name: str
+    description: str | None
+    mount_path: str
+    files: dict
+    project_overrides: dict | None
+    is_active: bool
+    created_at: str
+    updated_at: str
+
+
+@router.get("", summary="List config folders", description="Get all config folders for the current user.")
+async def list_config_folders(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """List config folders for the current user."""
+    query = select(ConfigFolder).where(ConfigFolder.user_id == user_id)
+    result = await session.execute(query)
+    folders = result.scalars().all()
+    
+    return {
+        "folders": [
+            {
+                "id": str(f.id),
+                "user_id": str(f.user_id),
+                "name": f.name,
+                "description": f.description,
+                "mount_path": f.mount_path,
+                "files": f.files,
+                "project_overrides": f.project_overrides,
+                "is_active": f.is_active,
+                "created_at": f.created_at.isoformat() if f.created_at else None,
+                "updated_at": f.updated_at.isoformat() if f.updated_at else None,
+            }
+            for f in folders
+        ]
+    }
+
+
+@router.post("", summary="Create config folder", description="Create a new config folder.", status_code=status.HTTP_201_CREATED)
+async def create_config_folder(
+    data: ConfigFolderCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a config folder."""
+    # Check for duplicate name
+    existing = await session.scalar(
+        select(ConfigFolder).where(
+            ConfigFolder.user_id == user_id,
+            ConfigFolder.name == data.name,
+        )
+    )
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"config folder with name '{data.name}' already exists"
+        )
+    
+    folder = ConfigFolder(
+        user_id=user_id,
+        name=data.name,
+        description=data.description,
+        mount_path=data.mount_path,
+        files=data.files,
+    )
+    session.add(folder)
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.put("/{folder_id}", summary="Update config folder", description="Update an existing config folder.")
+async def update_config_folder(
+    folder_id: uuid.UUID,
+    data: ConfigFolderUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    if data.name is not None:
+        folder.name = data.name
+    if data.description is not None:
+        folder.description = data.description
+    if data.mount_path is not None:
+        folder.mount_path = data.mount_path
+    if data.files is not None:
+        folder.files = data.files
+    if data.is_active is not None:
+        folder.is_active = data.is_active
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.delete("/{folder_id}", summary="Delete config folder", description="Delete a config folder.", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_folder(
+    folder_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    await session.delete(folder)
+    await session.commit()
+
+
+class ProjectOverrideWithId(ProjectOverrideCreate):
+    project_id: uuid.UUID = Field(description="Project ID for the override")
+
+
+@router.get("/{folder_id}", summary="Get config folder by ID", description="Get a single config folder by its ID.")
+async def get_config_folder(
+    folder_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get a config folder by ID."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.post("/{folder_id}/overrides", summary="Add project override", description="Add a project override to a config folder.")
+async def add_project_override(
+    folder_id: uuid.UUID,
+    data: ProjectOverrideWithId,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Add a project override to a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Initialize project_overrides if None
+    if folder.project_overrides is None:
+        folder.project_overrides = {}
+    
+    # Add/update override
+    override_data = {}
+    if data.mount_path is not None:
+        override_data["mount_path"] = data.mount_path
+    if data.files is not None:
+        override_data["files"] = data.files
+    
+    # Use a copy to trigger SQLAlchemy change detection on JSONB
+    current_overrides = dict(folder.project_overrides or {})
+    current_overrides[str(data.project_id)] = override_data
+    folder.project_overrides = current_overrides
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides,
+    }
+
+
+@router.put("/{folder_id}/overrides/{project_id}", summary="Update project override", description="Update a project override.")
+async def update_project_override(
+    folder_id: uuid.UUID,
+    project_id: uuid.UUID,
+    data: ProjectOverrideCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a project override."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Initialize project_overrides if None
+    if folder.project_overrides is None:
+        folder.project_overrides = {}
+    
+    # Update override
+    current_overrides = dict(folder.project_overrides or {})
+    override_data = current_overrides.get(str(project_id), {})
+    if data.mount_path is not None:
+        override_data["mount_path"] = data.mount_path
+    if data.files is not None:
+        override_data["files"] = data.files
+    
+    current_overrides[str(project_id)] = override_data
+    folder.project_overrides = current_overrides
+    
+    # Mark the field as modified to ensure SQLAlchemy detects the change
+    from sqlalchemy.orm.attributes import flag_modified
+    flag_modified(folder, "project_overrides")
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides,
+    }
+
+
+@router.delete("/{folder_id}/overrides/{project_id}", summary="Remove project override", description="Remove a project override.")
+async def remove_project_override(
+    folder_id: uuid.UUID,
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Remove a project override."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Remove override if exists
+    current_overrides = dict(folder.project_overrides or {})
+    if str(project_id) in current_overrides:
+        del current_overrides[str(project_id)]
+        folder.project_overrides = current_overrides
+        await session.commit()
+        await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides or {},
+    }

apps/api/src/api/dashboard.py

@@ -0,0 +1,65 @@
+import uuid
+
+from fastapi import APIRouter, Depends
+from sqlalchemy import func, select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.git_repository import GitRepository
+from src.models.project import Project
+from src.models.ssh_key import SSHKey
+
+router = APIRouter(prefix="/dashboard", tags=["dashboard"])
+
+
+@router.get(
+    "/summary",
+    summary="Get dashboard summary",
+    description="Get a summary of the user's projects, repositories, SSH keys, and recent activity.",
+)
+async def get_dashboard_summary(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get a summary of the user's dashboard data.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Dictionary with counts of projects, repositories, SSH keys, and recent activity.
+    """
+    # Count user's projects
+    projects_result = await session.execute(
+        select(func.count()).select_from(Project).where(Project.owner_id == user_id)
+    )
+    projects_count = projects_result.scalar() or 0
+
+    # Count user's repositories
+    repos_result = await session.execute(
+        select(func.count()).select_from(GitRepository).where(GitRepository.owner_id == user_id)
+    )
+    repos_count = repos_result.scalar() or 0
+
+    # Count user's SSH keys
+    ssh_keys_result = await session.execute(
+        select(func.count()).select_from(SSHKey).where(SSHKey.user_id == user_id)
+    )
+    ssh_keys_count = ssh_keys_result.scalar() or 0
+
+    # Get recent activity (latest 5 projects)
+    recent_projects = await session.execute(
+        select(Project)
+        .where(Project.owner_id == user_id)
+        .order_by(Project.created_at.desc())
+        .limit(5)
+    )
+    recent_activity = [f"Created project: {p.name}" for p in recent_projects.scalars().all()]
+
+    return {
+        "projects": projects_count,
+        "repositories": repos_count,
+        "sshKeys": ssh_keys_count,
+        "recentActivity": recent_activity,
+    }

apps/api/src/api/health.py

@@ -0,0 +1,149 @@
+"""Health check endpoints and models."""
+
+import time
+from datetime import datetime, timezone
+from typing import Any
+
+from fastapi import APIRouter, status
+from pydantic import BaseModel, Field
+from sqlalchemy import text
+
+from src.config import Settings
+from src.database import SessionLocal
+
+router = APIRouter()
+
+# Track start time for uptime
+_start_time = time.time()
+
+
+class DatabaseHealth(BaseModel):
+    """Database health check result."""
+
+    status: str = Field(description="Database health status", examples=["healthy"])
+    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
+
+
+class DiskHealth(BaseModel):
+    """Disk space health check result."""
+
+    status: str = Field(description="Disk health status", examples=["healthy"])
+    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
+    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
+
+
+class HealthChecks(BaseModel):
+    """Individual health checks."""
+
+    database: DatabaseHealth | None = None
+    disk: DiskHealth | None = None
+
+
+class HealthResponse(BaseModel):
+    """Overall health check response."""
+
+    status: str = Field(description="Overall health status", examples=["healthy"])
+    timestamp: str = Field(description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"])
+    version: str = Field(description="API version", examples=["0.1.0"])
+    checks: HealthChecks = Field(description="Individual health checks")
+    uptime_seconds: float = Field(description="Server uptime in seconds", examples=[3600.0])
+
+
+class DatabaseHealthResponse(BaseModel):
+    """Database-specific health check response."""
+
+    status: str = Field(description="Database health status", examples=["healthy"])
+    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
+
+
+@router.get(
+    "/health",
+    response_model=HealthResponse,
+    summary="Health check",
+    description="Returns overall system health status including database and disk checks.",
+    tags=["Health"],
+)
+async def health_check() -> dict[str, Any]:
+    """Check overall system health.
+
+    Returns:
+        HealthResponse with status, timestamp, version, checks, and uptime.
+    """
+    checks = HealthChecks()
+    overall_status = "healthy"
+
+    # Database check
+    try:
+        import time as time_module
+
+        start = time_module.perf_counter()
+        async with SessionLocal() as session:
+            await session.execute(text("SELECT 1"))
+        db_time = (time_module.perf_counter() - start) * 1000
+        checks.database = DatabaseHealth(
+            status="healthy",
+            response_time_ms=round(db_time, 2),
+        )
+    except Exception:
+        checks.database = DatabaseHealth(
+            status="unhealthy",
+            response_time_ms=0.0,
+        )
+        overall_status = "degraded"
+
+    # Disk check
+    try:
+        import shutil
+
+        disk = shutil.disk_usage("/")
+        free_gb = disk.free / (1024**3)
+        total_gb = disk.total / (1024**3)
+        disk_status = "healthy" if free_gb > 1.0 else "degraded"
+        if disk_status == "degraded":
+            overall_status = "degraded"
+        checks.disk = DiskHealth(
+            status=disk_status,
+            free_gb=round(free_gb, 2),
+            total_gb=round(total_gb, 2),
+        )
+    except Exception:
+        checks.disk = None
+
+    return 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()
+
+
+@router.get(
+    "/health/db",
+    response_model=DatabaseHealthResponse,
+    summary="Database health check",
+    description="Returns database-specific health status with response time.",
+    tags=["Health"],
+)
+async def health_check_db() -> dict[str, Any]:
+    """Check database health.
+
+    Returns:
+        DatabaseHealthResponse with status and response time.
+    """
+    import time as time_module
+
+    try:
+        start = time_module.perf_counter()
+        async with SessionLocal() as session:
+            await session.execute(text("SELECT 1"))
+        db_time = (time_module.perf_counter() - start) * 1000
+        return DatabaseHealthResponse(
+            status="healthy",
+            response_time_ms=round(db_time, 2),
+        ).model_dump()
+    except Exception:
+        return DatabaseHealthResponse(
+            status="unhealthy",
+            response_time_ms=0.0,
+        ).model_dump()

apps/api/src/api/instance_proxy.py

@@ -0,0 +1,125 @@
+"""Instance proxy router for forwarding HTTP requests to running containers."""
+
+import logging
+import uuid
+from typing import Any
+
+import httpx
+from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.tool_instance import ToolInstance
+from src.models.tool_type import ToolType
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/instances", tags=["instance-proxy"])
+
+
+async def _proxy_request(
+    request: Request,
+    instance_id: uuid.UUID,
+    path: str,
+    user_id: uuid.UUID,
+    session: AsyncSession,
+) -> Response:
+    """Proxy an HTTP request to a running instance."""
+    instance = await session.get(ToolInstance, instance_id)
+    if instance is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
+        )
+
+    # Verify ownership
+    if instance.owner_id != user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN,
+            detail="not authorized to access this instance",
+        )
+
+    if instance.status != "running" or not instance.container_name:
+        raise HTTPException(
+            status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
+            detail="instance is not running",
+        )
+
+    # Get the tool type to find the internal port
+    tool_type = await session.get(ToolType, instance.tool_type_id)
+    internal_port = tool_type.default_port if tool_type and tool_type.default_port else instance.port
+
+    # Build target URL using internal port
+    target_url = f"http://{instance.container_name}:{internal_port}"
+    if path:
+        target_url += f"/{path}"
+
+    # Get query string
+    query_string = str(request.query_params)
+    if query_string:
+        target_url += f"?{query_string}"
+
+    # Forward headers (excluding host and cookies)
+    headers: dict[str, str] = {}
+    for key, value in request.headers.items():
+        if key.lower() not in ("host", "cookie", "content-length"):
+            headers[key] = value
+
+    # Forward the request
+    try:
+        async with httpx.AsyncClient() as client:
+            body = await request.body()
+            response = await client.request(
+                method=request.method,
+                url=target_url,
+                headers=headers,
+                content=body,
+                follow_redirects=False,
+                timeout=30.0,
+            )
+    except Exception as exc:
+        logger.error("Proxy error to %s: %s", target_url, exc)
+        raise HTTPException(
+            status_code=status.HTTP_502_BAD_GATEWAY,
+            detail=f"failed to reach instance: {exc}",
+        )
+
+    # Build response
+    response_headers = dict(response.headers)
+    # Remove hop-by-hop headers
+    for header in ("content-encoding", "transfer-encoding", "connection"):
+        response_headers.pop(header, None)
+
+    return Response(
+        content=response.content,
+        status_code=response.status_code,
+        headers=response_headers,
+    )
+
+
+@router.get("/{instance_id}/proxy/{path:path}")
+@router.post("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.put("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.delete("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.patch("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.head("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.options("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+async def proxy_to_instance(
+    request: Request,
+    instance_id: uuid.UUID,
+    path: str = "",
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Response:
+    """Proxy requests to a running tool instance.
+
+    Args:
+        request: The incoming HTTP request.
+        instance_id: UUID of the instance.
+        path: The path to proxy to the instance.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Response from the proxied instance.
+    """
+    return await _proxy_request(request, instance_id, path, user_id, session)

apps/api/src/api/projects.py

@@ -1,16 +1,13 @@
 import os
 import shutil
 import uuid
-from typing import Annotated
 
-from fastapi import APIRouter, Cookie, Depends, HTTPException, Response, status
+from fastapi import APIRouter, Depends, HTTPException, Response, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.jwt_service import decode_access_token
-from src.config import Settings
-from src.database import SessionLocal
+from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models.git_repository import GitRepository
 from src.models.project import Project
 from src.models.ssh_key import SSHKey
@@ -19,25 +16,8 @@ from src.models.user import User
 router = APIRouter(prefix="/projects", tags=["projects"])
 
 
-async def get_db_session():
-    async with SessionLocal() as session:
-        yield session
-
-
-async def get_current_user_id(
-    access_token: Annotated[str | None, Cookie()] = None,
-) -> uuid.UUID:
-    if not access_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing access token")
-
-    try:
-        claims = decode_access_token(settings=Settings(), token=access_token)
-        return uuid.UUID(str(claims["sub"]))
-    except Exception:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid access token")
-
-
 async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
     user = await session.get(User, user_id)
     if user is None:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
@@ -68,12 +48,28 @@ class SetDefaultSSHKeyRequest(BaseModel):
     ssh_key_id: uuid.UUID
 
 
-@router.post("", response_model=ProjectResponse, status_code=status.HTTP_201_CREATED)
+@router.post(
+    "",
+    response_model=ProjectResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create a new project",
+    description="Create a new project for the authenticated user.",
+)
 async def create_project(
     data: ProjectCreate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
+    """Create a new project.
+
+    Args:
+        data: Project creation data including name and optional description.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The newly created project.
+    """
     user = await _get_user(session, user_id)
     project = Project(
         name=data.name,
@@ -87,21 +83,73 @@ async def create_project(
     return project
 
 
-@router.get("", response_model=list[ProjectResponse])
+@router.get(
+    "",
+    response_model=list[ProjectResponse],
+    summary="List all projects",
+    description="Retrieve all projects owned by the authenticated user.",
+)
 async def list_projects(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[Project]:
+    """List all projects for the authenticated user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        List of projects owned by the user.
+    """
     user = await _get_user(session, user_id)
     result = await session.execute(select(Project).where(Project.owner_id == user.id))
     return list(result.scalars().all())
 
 
+@router.get(
+    "/{project_id}",
+    response_model=ProjectResponse,
+    summary="Get a project",
+    description="Retrieve a specific project by ID.",
+)
+async def get_project(
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Project:
+    """Get a specific project by ID.
+
+    Args:
+        project_id: UUID of the project to retrieve.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The requested project.
+    """
+    await _get_user(session, user_id)
+    return await _get_owned_project(project_id, user_id, session)
+
+
 async def _get_owned_project(
     project_id: uuid.UUID,
     user_id: uuid.UUID,
     session: AsyncSession,
 ) -> Project:
+    """Fetch a project and verify ownership.
+
+    Args:
+        project_id: UUID of the project.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The project if found and owned by the user.
+
+    Raises:
+        HTTPException: If project not found or user is not the owner.
+    """
     project = await session.get(Project, project_id)
     if project is None:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="project not found")
@@ -110,13 +158,29 @@ async def _get_owned_project(
     return project
 
 
-@router.patch("/{project_id}", response_model=ProjectResponse)
+@router.patch(
+    "/{project_id}",
+    response_model=ProjectResponse,
+    summary="Update a project",
+    description="Update a project's name or description.",
+)
 async def update_project(
     project_id: uuid.UUID,
     data: ProjectUpdate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
+    """Update a project.
+
+    Args:
+        project_id: UUID of the project to update.
+        data: Project update data with optional name and description.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated project.
+    """
     await _get_user(session, user_id)
     project = await _get_owned_project(project_id, user_id, session)
 
@@ -130,12 +194,27 @@ async def update_project(
     return project
 
 
-@router.delete("/{project_id}", status_code=status.HTTP_204_NO_CONTENT)
+@router.delete(
+    "/{project_id}",
+    status_code=status.HTTP_204_NO_CONTENT,
+    summary="Delete a project",
+    description="Delete a project and all its associated repositories.",
+)
 async def delete_project(
     project_id: uuid.UUID,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Response:
+    """Delete a project and all its repositories.
+
+    Args:
+        project_id: UUID of the project to delete.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Empty response with 204 status code.
+    """
     await _get_user(session, user_id)
     project = await _get_owned_project(project_id, user_id, session)
 
@@ -152,13 +231,29 @@ async def delete_project(
     return Response(status_code=status.HTTP_204_NO_CONTENT)
 
 
-@router.patch("/{project_id}/default-ssh-key", response_model=ProjectResponse)
+@router.patch(
+    "/{project_id}/default-ssh-key",
+    response_model=ProjectResponse,
+    summary="Set default SSH key",
+    description="Set the default SSH key for a project.",
+)
 async def set_default_ssh_key(
     project_id: uuid.UUID,
     data: SetDefaultSSHKeyRequest,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
+    """Set the default SSH key for a project.
+
+    Args:
+        project_id: UUID of the project.
+        data: Request containing the SSH key ID to set as default.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated project.
+    """
     user = await _get_user(session, user_id)
     project = await _get_owned_project(project_id, user_id, session)
 

apps/api/src/api/ssh_keys.py

@@ -1,43 +1,24 @@
 import uuid
 from datetime import datetime
-from typing import Annotated
 
 from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey
-from fastapi import APIRouter, Cookie, Depends, HTTPException, status
+from fastapi import APIRouter, Depends, HTTPException, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.jwt_service import decode_access_token
+from src.auth.dependencies import get_current_user_id, get_db_session
 from src.config import Settings
-from src.database import SessionLocal
 from src.models.ssh_key import SSHKey
 from src.models.user import User
 
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
 
 
-async def get_db_session():
-    async with SessionLocal() as session:
-        yield session
-
-
-async def get_current_user_id(
-    access_token: Annotated[str | None, Cookie()] = None,
-) -> uuid.UUID:
-    if not access_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing access token")
-
-    try:
-        claims = decode_access_token(settings=Settings(), token=access_token)
-        return uuid.UUID(str(claims["sub"]))
-    except Exception:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid access token")
-
-
 async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
     user = await session.get(User, user_id)
     if user is None:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
@@ -45,12 +26,24 @@ async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
 
 
 def _get_fernet() -> Fernet:
+    """Generate a valid Fernet key from the session secret."""
+    import base64
+    import hashlib
+    
     settings = Settings()
-    key = settings.jwt_secret[:32].ljust(32, "=")
-    return Fernet(key.encode())
+    # Derive a 32-byte key from the session secret using SHA256
+    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
+    # Base64 encode it for Fernet (must be 32 url-safe base64-encoded bytes)
+    key = base64.urlsafe_b64encode(key_bytes)
+    return Fernet(key)
 
 
 def generate_ssh_key_pair() -> tuple[str, str]:
+    """Generate a new Ed25519 SSH key pair.
+
+    Returns:
+        Tuple of (private_key, public_key) as strings.
+    """
     private_key = Ed25519PrivateKey.generate()
     public_key = private_key.public_key()
 
@@ -81,12 +74,28 @@ class SSHKeyResponse(BaseModel):
     created_at: datetime
 
 
-@router.post("", response_model=SSHKeyResponse, status_code=status.HTTP_201_CREATED)
+@router.post(
+    "",
+    response_model=SSHKeyResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create SSH key",
+    description="Generate a new Ed25519 SSH key pair for the authenticated user.",
+)
 async def create_ssh_key(
     data: SSHKeyCreate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> SSHKey:
+    """Create a new SSH key pair.
+
+    Args:
+        data: SSH key creation data including the key name.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The newly created SSH key with public key exposed.
+    """
     user = await _get_user(session, user_id)
     private_key, public_key = generate_ssh_key_pair()
 
@@ -105,22 +114,51 @@ async def create_ssh_key(
     return ssh_key
 
 
-@router.get("", response_model=list[SSHKeyResponse])
+@router.get(
+    "",
+    response_model=list[SSHKeyResponse],
+    summary="List SSH keys",
+    description="List all SSH keys for the authenticated user.",
+)
 async def list_ssh_keys(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[SSHKey]:
+    """List all SSH keys for the authenticated user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        List of SSH keys owned by the user.
+    """
     user = await _get_user(session, user_id)
     result = await session.execute(select(SSHKey).where(SSHKey.user_id == user.id))
     return list(result.scalars().all())
 
 
-@router.delete("/{key_id}", status_code=status.HTTP_204_NO_CONTENT)
+@router.delete(
+    "/{key_id}",
+    status_code=status.HTTP_204_NO_CONTENT,
+    summary="Delete SSH key",
+    description="Delete an SSH key by ID.",
+)
 async def delete_ssh_key(
     key_id: uuid.UUID,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
+    """Delete an SSH key.
+
+    Args:
+        key_id: UUID of the SSH key to delete.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        None with 204 status code.
+    """
     user = await _get_user(session, user_id)
     ssh_key = await session.get(SSHKey, key_id)
     if ssh_key is None or ssh_key.user_id != user.id:

apps/api/src/api/terminal.py

@@ -0,0 +1,124 @@
+"""WebSocket terminal endpoint for tool instances."""
+
+import asyncio
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, WebSocket, WebSocketDisconnect, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_db_session
+from src.models.tool_instance import ToolInstance
+from src.services.terminal_manager import terminal_manager
+
+router = APIRouter()
+logger = logging.getLogger(__name__)
+
+
+@router.websocket(
+    "/ws/tool-instances/{instance_id}/terminal",
+)
+async def terminal_websocket(
+    websocket: WebSocket,
+    instance_id: str,
+    db_session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """WebSocket endpoint for terminal access to a tool instance.
+
+    Provides an interactive terminal session inside a running tool instance container.
+
+    Args:
+        websocket: The WebSocket connection.
+        instance_id: UUID string of the tool instance.
+        db_session: Database session.
+
+    Returns:
+        None. Communicates via WebSocket messages.
+    """
+    logger.info("Terminal WebSocket connection attempt for instance %s", instance_id)
+    await websocket.accept()
+
+    try:
+        # Parse instance_id
+        instance_uuid = uuid.UUID(instance_id)
+    except ValueError:
+        logger.error("Invalid instance ID: %s", instance_id)
+        await websocket.close(code=4001, reason="Invalid instance ID")
+        return
+
+    # Authenticate user from session cookie
+    user_id = await _get_user_from_websocket(websocket, db_session)
+    if user_id is None:
+        logger.warning("Unauthorized terminal access attempt for instance %s", instance_id)
+        await websocket.close(code=4003, reason="Unauthorized")
+        return
+
+    # Get instance and verify ownership
+    instance = await db_session.get(ToolInstance, instance_uuid)
+    if instance is None:
+        logger.warning("Instance %s not found", instance_id)
+        await websocket.close(code=4004, reason="Instance not found")
+        return
+
+    if instance.owner_id != user_id:
+        logger.warning("Forbidden terminal access for instance %s by user %s", instance_id, user_id)
+        await websocket.close(code=4003, reason="Forbidden")
+        return
+
+    if instance.status != "running" or not instance.container_id:
+        logger.warning("Instance %s not running (status=%s, container_id=%s)", instance_id, instance.status, instance.container_id)
+        await websocket.close(code=4004, reason="Instance not running")
+        return
+
+    logger.info("Creating terminal session for instance %s (container_id=%s)", instance_id, instance.container_id)
+    # Create terminal session
+    try:
+        session = await terminal_manager.create_session(
+            instance_uuid,
+            instance.container_id,
+            websocket,
+        )
+        logger.info("Terminal session created successfully for instance %s", instance_id)
+
+        # Send connected status
+        await websocket.send_json({"type": "status", "status": "connected"})
+
+        # Keep connection alive until session ends
+        # The terminal_manager handles I/O loops, we just wait here
+        while session.is_alive() and not session._closed:
+            await asyncio.sleep(0.5)
+
+    except Exception as exc:
+        logger.error("Terminal session error for instance %s: %s", instance_id, str(exc), exc_info=True)
+        await websocket.close(code=4000, reason=f"Error: {exc}")
+    finally:
+        # Cleanup will be handled by the session manager
+        pass
+
+
+async def _get_user_from_websocket(
+    websocket: WebSocket,
+    db_session: AsyncSession,
+) -> uuid.UUID | None:
+    """Extract and validate user ID from session cookie in WebSocket.
+
+    Args:
+        websocket: The WebSocket connection.
+        db_session: Database session.
+
+    Returns:
+        The user's UUID if authenticated, None otherwise.
+    """
+    from src.auth.session import decode_session_cookie
+    from src.config import Settings
+
+    session_cookie = websocket.cookies.get("session")
+    if not session_cookie:
+        return None
+
+    settings = Settings()
+    try:
+        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+        return uuid.UUID(str(payload["user_id"]))
+    except (ValueError, KeyError):
+        return None

apps/api/src/api/tool_configs.py

@@ -0,0 +1,322 @@
+"""Tool configuration API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from pydantic import BaseModel, Field, field_validator
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.tool_config import ToolConfig
+from src.models.tool_type import ToolType
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/tool-configs", tags=["tool-configs"])
+
+
+class ToolConfigCreate(BaseModel):
+    tool_type_id: str = Field(description="UUID of the tool type")
+    project_id: str | None = Field(default=None, description="Optional project ID for project-scoped config")
+    key: str = Field(description="Config key name")
+    value: str = Field(description="Config value")
+    config_type: str = Field(default="env", description="Type: env or file")
+    file_path: str | None = Field(default=None, description="File path for file-type configs")
+    port_override: int | None = Field(default=None, description="Port override (1-65535)")
+    start_command: str | None = Field(default=None, description="Override container start command")
+    working_directory: str | None = Field(default=None, description="Working directory inside container")
+    environment_variables: dict | None = Field(default=None, description="Environment variables as JSON object")
+    volumes: list[dict] | None = Field(default=None, description="Volume mounts as JSON array")
+
+    @field_validator("port_override")
+    @classmethod
+    def validate_port(cls, v: int | None) -> int | None:
+        if v is None:
+            return v
+        if v < 1 or v > 65535:
+            raise ValueError("Port must be between 1 and 65535")
+        return v
+
+    @field_validator("environment_variables")
+    @classmethod
+    def validate_env_vars(cls, v: dict | None) -> dict | None:
+        if v is None:
+            return v
+        if not isinstance(v, dict):
+            raise ValueError("environment_variables must be a JSON object")
+        return v
+
+    @field_validator("volumes")
+    @classmethod
+    def validate_volumes(cls, v: list | None) -> list | None:
+        if v is None:
+            return v
+        if not isinstance(v, list):
+            raise ValueError("volumes must be a JSON array")
+        for i, vol in enumerate(v):
+            if not isinstance(vol, dict):
+                raise ValueError(f"Volume at index {i} must be an object")
+            if "source" not in vol:
+                raise ValueError(f"Volume at index {i} must have 'source' field")
+            if "target" not in vol:
+                raise ValueError(f"Volume at index {i} must have 'target' field")
+        return v
+
+
+class ToolConfigUpdate(BaseModel):
+    key: str | None = Field(default=None, description="Config key name")
+    value: str | None = Field(default=None, description="Config value")
+    config_type: str | None = Field(default=None, description="Type: env or file")
+    file_path: str | None = Field(default=None, description="File path for file-type configs")
+    port_override: int | None = Field(default=None, description="Port override (1-65535)")
+    start_command: str | None = Field(default=None, description="Override container start command")
+    working_directory: str | None = Field(default=None, description="Working directory inside container")
+    environment_variables: dict | None = Field(default=None, description="Environment variables as JSON object")
+    volumes: list[dict] | None = Field(default=None, description="Volume mounts as JSON array")
+
+    @field_validator("port_override")
+    @classmethod
+    def validate_port(cls, v: int | None) -> int | None:
+        if v is None:
+            return v
+        if v < 1 or v > 65535:
+            raise ValueError("Port must be between 1 and 65535")
+        return v
+
+    @field_validator("environment_variables")
+    @classmethod
+    def validate_env_vars(cls, v: dict | None) -> dict | None:
+        if v is None:
+            return v
+        if not isinstance(v, dict):
+            raise ValueError("environment_variables must be a JSON object")
+        return v
+
+    @field_validator("volumes")
+    @classmethod
+    def validate_volumes(cls, v: list | None) -> list | None:
+        if v is None:
+            return v
+        if not isinstance(v, list):
+            raise ValueError("volumes must be a JSON array")
+        for i, vol in enumerate(v):
+            if not isinstance(vol, dict):
+                raise ValueError(f"Volume at index {i} must be an object")
+            if "source" not in vol:
+                raise ValueError(f"Volume at index {i} must have 'source' field")
+            if "target" not in vol:
+                raise ValueError(f"Volume at index {i} must have 'target' field")
+        return v
+
+
+class ToolConfigResponse(BaseModel):
+    id: str
+    tool_type_id: str
+    project_id: str | None
+    key: str
+    value: str
+    config_type: str
+    file_path: str | None
+    port_override: int | None
+    start_command: str | None
+    working_directory: str | None
+    environment_variables: dict | None
+    volumes: list[dict] | None
+
+
+@router.get("", summary="List tool configs", description="Get all tool configs for the current user.")
+async def list_configs(
+    tool_type_id: str | None = None,
+    project_id: str | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list:
+    """List tool configs for the current user."""
+    query = select(ToolConfig).where(ToolConfig.user_id == user_id)
+    
+    if tool_type_id:
+        query = query.where(ToolConfig.tool_type_id == uuid.UUID(tool_type_id))
+    if project_id:
+        query = query.where(ToolConfig.project_id == uuid.UUID(project_id))
+    else:
+        # If no project specified, get only global configs (project_id is None)
+        query = query.where(ToolConfig.project_id.is_(None))
+    
+    result = await session.execute(query)
+    configs = result.scalars().all()
+    
+    return [
+        {
+            "id": str(c.id),
+            "tool_type_id": str(c.tool_type_id),
+            "project_id": str(c.project_id) if c.project_id else None,
+            "key": c.key,
+            "value": c.value,
+            "config_type": c.config_type,
+            "file_path": c.file_path,
+            "port_override": c.port_override,
+            "start_command": c.start_command,
+            "working_directory": c.working_directory,
+            "environment_variables": c.environment_variables,
+            "volumes": c.volumes,
+        }
+        for c in configs
+    ]
+
+
+@router.post("", summary="Create tool config", description="Create a new tool config.", status_code=status.HTTP_201_CREATED)
+async def create_config(
+    data: ToolConfigCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a tool config."""
+    # Verify tool type exists
+    tool_type = await session.get(ToolType, uuid.UUID(data.tool_type_id))
+    if tool_type is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    
+    # Check for existing config with same key
+    query = select(ToolConfig).where(
+        ToolConfig.user_id == user_id,
+        ToolConfig.tool_type_id == uuid.UUID(data.tool_type_id),
+        ToolConfig.key == data.key,
+    )
+    if data.project_id:
+        query = query.where(ToolConfig.project_id == uuid.UUID(data.project_id))
+    else:
+        query = query.where(ToolConfig.project_id.is_(None))
+    
+    existing = await session.scalar(query)
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"config with key '{data.key}' already exists"
+        )
+    
+    config = ToolConfig(
+        user_id=user_id,
+        tool_type_id=uuid.UUID(data.tool_type_id),
+        project_id=uuid.UUID(data.project_id) if data.project_id else None,
+        key=data.key,
+        value=data.value,
+        config_type=data.config_type,
+        file_path=data.file_path,
+        port_override=data.port_override,
+        start_command=data.start_command,
+        working_directory=data.working_directory,
+        environment_variables=data.environment_variables,
+        volumes=data.volumes,
+    )
+    session.add(config)
+    await session.commit()
+    await session.refresh(config)
+    
+    return {
+        "id": str(config.id),
+        "tool_type_id": str(config.tool_type_id),
+        "project_id": str(config.project_id) if config.project_id else None,
+        "key": config.key,
+        "value": config.value,
+        "config_type": config.config_type,
+        "file_path": config.file_path,
+        "port_override": config.port_override,
+        "start_command": config.start_command,
+        "working_directory": config.working_directory,
+        "environment_variables": config.environment_variables,
+        "volumes": config.volumes,
+    }
+
+
+@router.put("/{config_id}", summary="Update tool config", description="Update an existing tool config.")
+async def update_config(
+    config_id: uuid.UUID,
+    data: ToolConfigUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a tool config."""
+    config = await session.get(ToolConfig, config_id)
+    if config is None or config.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config not found")
+    
+    if data.key is not None:
+        config.key = data.key
+    if data.value is not None:
+        config.value = data.value
+    if data.config_type is not None:
+        config.config_type = data.config_type
+    if data.file_path is not None:
+        config.file_path = data.file_path
+    if data.port_override is not None:
+        config.port_override = data.port_override
+    if data.start_command is not None:
+        config.start_command = data.start_command
+    if data.working_directory is not None:
+        config.working_directory = data.working_directory
+    if data.environment_variables is not None:
+        config.environment_variables = data.environment_variables
+    if data.volumes is not None:
+        config.volumes = data.volumes
+    
+    await session.commit()
+    await session.refresh(config)
+    
+    return {
+        "id": str(config.id),
+        "tool_type_id": str(config.tool_type_id),
+        "project_id": str(config.project_id) if config.project_id else None,
+        "key": config.key,
+        "value": config.value,
+        "config_type": config.config_type,
+        "file_path": config.file_path,
+        "port_override": config.port_override,
+        "start_command": config.start_command,
+        "working_directory": config.working_directory,
+        "environment_variables": config.environment_variables,
+        "volumes": config.volumes,
+    }
+
+
+@router.get("/defaults/{tool_type_id}", summary="Get default configs", description="Get suggested default configs for a tool type.")
+async def get_default_configs(
+    tool_type_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get suggested default configs for a tool type."""
+    tool_type = await session.get(ToolType, uuid.UUID(tool_type_id))
+    if tool_type is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    
+    # Return suggested defaults based on required_variables
+    defaults = []
+    for var in tool_type.required_variables:
+        defaults.append({
+            "key": var,
+            "value": "",
+            "config_type": "env",
+            "description": f"Required variable: {var}",
+        })
+    
+    return {
+        "tool_type_id": tool_type_id,
+        "suggested_configs": defaults,
+    }
+
+
+@router.delete("/{config_id}", summary="Delete tool config", description="Delete a tool config.")
+async def delete_config(
+    config_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete a tool config."""
+    config = await session.get(ToolConfig, config_id)
+    if config is None or config.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config not found")
+    
+    await session.delete(config)
+    await session.commit()

apps/api/src/api/tool_types.py

@@ -1,40 +1,21 @@
 import uuid
-from typing import Annotated
+from datetime import datetime
 
 import yaml
-from fastapi import APIRouter, Cookie, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict, field_validator
+from fastapi import APIRouter, Depends, HTTPException, status
+from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.jwt_service import decode_access_token
-from src.config import Settings
-from src.database import SessionLocal
+from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models.tool_type import ToolType
 from src.models.user import User
 
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])
 
 
-async def get_db_session():
-    async with SessionLocal() as session:
-        yield session
-
-
-async def get_current_user_id(
-    access_token: Annotated[str | None, Cookie()] = None,
-) -> uuid.UUID:
-    if not access_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing access token")
-
-    try:
-        claims = decode_access_token(settings=Settings(), token=access_token)
-        return uuid.UUID(str(claims["sub"]))
-    except Exception:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid access token")
-
-
 async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
     user = await session.get(User, user_id)
     if user is None:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
@@ -42,6 +23,11 @@ async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
 
 
 async def _require_admin(user: User) -> None:
+    """Check if user has admin privileges.
+
+    For now, all authenticated users can manage tool types.
+    In production, this should check user.role or similar.
+    """
     # For now, all authenticated users can manage tool types
     # In production, check user.role or similar
     pass
@@ -51,12 +37,33 @@ class ToolTypeCreate(BaseModel):
     name: str
     display_name: str
     description: str | None = None
-    compose_template: str
+    default_port: int
+    definition_type: str = "compose"
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
     required_variables: list[str] = []
+    category: str = "other"
+    interfaces: list[str] = ["web"]
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str) -> str:
+        if v not in ("compose", "dockerfile"):
+            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
+        return v
 
     @field_validator("compose_template")
     @classmethod
-    def validate_compose_template(cls, v: str) -> str:
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+        
+        if v is None:
+            raise ValueError("compose_template is required when definition_type is 'compose'")
+        
         try:
             parsed = yaml.safe_load(v)
         except yaml.YAMLError as e:
@@ -73,18 +80,79 @@ class ToolTypeCreate(BaseModel):
         
         return v
 
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "dockerfile":
+            return v
+        
+        if v is None:
+            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
+        
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+        
+        return v
+
+    @field_validator("default_port")
+    @classmethod
+    def validate_default_port(cls, v: int, info) -> int:
+        if v <= 0 or v > 65535:
+            raise ValueError("Port must be between 1 and 65535")
+        
+        # Get compose_template from the model data
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+        
+        template = data.get("compose_template")
+        if not template:
+            return v
+        
+        try:
+            parsed = yaml.safe_load(template)
+        except yaml.YAMLError:
+            return v
+        
+        # Check if the port is exposed in any service
+        port_str = str(v)
+        port_exposed = False
+        
+        if isinstance(parsed, dict) and "services" in parsed:
+            for service_name, service_config in parsed["services"].items():
+                if isinstance(service_config, dict) and "ports" in service_config:
+                    for port_mapping in service_config["ports"]:
+                        if isinstance(port_mapping, str):
+                            # Format: "8443:8443" or "8443"
+                            if port_str in port_mapping:
+                                port_exposed = True
+                                break
+                        elif isinstance(port_mapping, int) and port_mapping == v:
+                            port_exposed = True
+                            break
+                if port_exposed:
+                    break
+        
+        if not port_exposed:
+            raise ValueError(f"Port {v} is not exposed in the compose template. Add it to the 'ports' section.")
+        
+        return v
+
     @field_validator("required_variables")
     @classmethod
     def validate_required_variables(cls, v: list[str], info) -> list[str]:
         if not v:
             return v
         
-        # Get compose_template from the model data
         data = info.data
-        if "compose_template" not in data:
+        if data.get("definition_type") != "compose":
+            return v
+        
+        template = data.get("compose_template")
+        if not template:
             return v
         
-        template = data["compose_template"]
         for var in v:
             placeholder = f"{{{{{var}}}}}"
             if placeholder not in template:
@@ -92,19 +160,48 @@ class ToolTypeCreate(BaseModel):
         
         return v
 
+    @model_validator(mode="after")
+    def validate_templates(self) -> "ToolTypeCreate":
+        if self.definition_type == "dockerfile" and self.dockerfile_template is None:
+            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
+        if self.definition_type == "compose" and self.compose_template is None:
+            raise ValueError("compose_template is required when definition_type is 'compose'")
+        return self
+
 
 class ToolTypeUpdate(BaseModel):
     display_name: str | None = None
     description: str | None = None
+    default_port: int | None = None
+    definition_type: str | None = None
     compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
     required_variables: list[str] | None = None
+    category: str | None = None
+    interfaces: list[str] | None = None
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("compose", "dockerfile"):
+            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
+        return v
 
     @field_validator("compose_template")
     @classmethod
-    def validate_compose_template(cls, v: str | None) -> str | None:
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
         if v is None:
             return v
         
+        data = info.data
+        definition_type = data.get("definition_type")
+        if definition_type and definition_type != "compose":
+            return v
+        
         try:
             parsed = yaml.safe_load(v)
         except yaml.YAMLError as e:
@@ -121,6 +218,22 @@ class ToolTypeUpdate(BaseModel):
         
         return v
 
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        
+        data = info.data
+        definition_type = data.get("definition_type")
+        if definition_type and definition_type != "dockerfile":
+            return v
+        
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+        
+        return v
+
 
 class ToolTypeResponse(BaseModel):
     model_config = ConfigDict(from_attributes=True)
@@ -129,20 +242,43 @@ class ToolTypeResponse(BaseModel):
     name: str
     display_name: str
     description: str | None
-    compose_template: str
+    category: str
+    interfaces: list[str]
+    default_port: int
+    definition_type: str
+    compose_template: str | None
+    dockerfile_template: str | None
+    build_context: dict | None
+    readiness_probe: dict | None
     required_variables: list[str]
     is_builtin: bool
     created_by_id: uuid.UUID | None
-    created_at: str
-    updated_at: str
+    created_at: datetime
+    updated_at: datetime
 
 
-@router.post("", response_model=ToolTypeResponse, status_code=status.HTTP_201_CREATED)
+@router.post(
+    "",
+    response_model=ToolTypeResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create tool type",
+    description="Create a new custom tool type with a Docker Compose template.",
+)
 async def create_tool_type(
     data: ToolTypeCreate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
+    """Create a new tool type.
+
+    Args:
+        data: Tool type creation data including name, display name, and compose template.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The newly created tool type.
+    """
     user = await _get_user(session, user_id)
     await _require_admin(user)
     
@@ -155,8 +291,15 @@ async def create_tool_type(
         name=data.name,
         display_name=data.display_name,
         description=data.description,
+        default_port=data.default_port,
+        definition_type=data.definition_type,
         compose_template=data.compose_template,
+        dockerfile_template=data.dockerfile_template,
+        build_context=data.build_context,
+        readiness_probe=data.readiness_probe,
         required_variables=data.required_variables,
+        category=data.category,
+        interfaces=data.interfaces,
         is_builtin=False,
         created_by_id=user.id,
     )
@@ -166,22 +309,51 @@ async def create_tool_type(
     return tool_type
 
 
-@router.get("", response_model=list[ToolTypeResponse])
+@router.get(
+    "",
+    response_model=list[ToolTypeResponse],
+    summary="List tool types",
+    description="List all available tool types including built-in and custom ones.",
+)
 async def list_tool_types(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[ToolType]:
+    """List all tool types.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        List of all tool types ordered by name.
+    """
     await _get_user(session, user_id)
     result = await session.execute(select(ToolType).order_by(ToolType.name))
     return list(result.scalars().all())
 
 
-@router.get("/{tool_type_id}", response_model=ToolTypeResponse)
+@router.get(
+    "/{tool_type_id}",
+    response_model=ToolTypeResponse,
+    summary="Get tool type",
+    description="Get a specific tool type by ID.",
+)
 async def get_tool_type(
     tool_type_id: uuid.UUID,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
+    """Get a specific tool type by ID.
+
+    Args:
+        tool_type_id: UUID of the tool type to retrieve.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The requested tool type.
+    """
     await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
@@ -189,13 +361,29 @@ async def get_tool_type(
     return tool_type
 
 
-@router.put("/{tool_type_id}", response_model=ToolTypeResponse)
+@router.put(
+    "/{tool_type_id}",
+    response_model=ToolTypeResponse,
+    summary="Update tool type",
+    description="Update a custom tool type. Built-in tool types cannot be modified.",
+)
 async def update_tool_type(
     tool_type_id: uuid.UUID,
     data: ToolTypeUpdate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
+    """Update a tool type.
+
+    Args:
+        tool_type_id: UUID of the tool type to update.
+        data: Tool type update data with optional fields.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated tool type.
+    """
     user = await _get_user(session, user_id)
     await _require_admin(user)
     
@@ -208,26 +396,68 @@ async def update_tool_type(
     
     update_data = data.model_dump(exclude_unset=True)
     
-    # Validate required variables if both are being updated
-    if "required_variables" in update_data and "compose_template" in update_data:
-        template = update_data["compose_template"]
-        for var in update_data["required_variables"]:
-            placeholder = f"{{{{{var}}}}}"
-            if placeholder not in template:
-                raise HTTPException(
-                    status_code=status.HTTP_400_BAD_REQUEST,
-                    detail=f"Required variable '{var}' not found in compose template"
-                )
-    elif "required_variables" in update_data:
-        # Only updating variables, check against existing template
-        template = tool_type.compose_template
-        for var in update_data["required_variables"]:
-            placeholder = f"{{{{{var}}}}}"
-            if placeholder not in template:
-                raise HTTPException(
-                    status_code=status.HTTP_400_BAD_REQUEST,
-                    detail=f"Required variable '{var}' not found in compose template"
-                )
+    # Validate port if being updated
+    if "default_port" in update_data:
+        new_port = update_data["default_port"]
+        if new_port <= 0 or new_port > 65535:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Port must be between 1 and 65535"
+            )
+        
+        # Only validate port exposure for compose definitions
+        definition_type = update_data.get("definition_type", tool_type.definition_type)
+        if definition_type == "compose":
+            template = update_data.get("compose_template", tool_type.compose_template)
+            if template:
+                try:
+                    parsed = yaml.safe_load(template)
+                except yaml.YAMLError:
+                    parsed = None
+                
+                if parsed and isinstance(parsed, dict) and "services" in parsed:
+                    port_str = str(new_port)
+                    port_exposed = False
+                    for service_config in parsed["services"].values():
+                        if isinstance(service_config, dict) and "ports" in service_config:
+                            for port_mapping in service_config["ports"]:
+                                if isinstance(port_mapping, str) and port_str in port_mapping:
+                                    port_exposed = True
+                                    break
+                                elif isinstance(port_mapping, int) and port_mapping == new_port:
+                                    port_exposed = True
+                                    break
+                        if port_exposed:
+                            break
+                    
+                    if not port_exposed:
+                        raise HTTPException(
+                            status_code=status.HTTP_400_BAD_REQUEST,
+                            detail=f"Port {new_port} is not exposed in the compose template"
+                        )
+    
+    # Validate required variables for compose definitions
+    definition_type = update_data.get("definition_type", tool_type.definition_type)
+    if definition_type == "compose":
+        if "required_variables" in update_data and "compose_template" in update_data:
+            template = update_data["compose_template"]
+            for var in update_data["required_variables"]:
+                placeholder = f"{{{{{var}}}}}"
+                if placeholder not in template:
+                    raise HTTPException(
+                        status_code=status.HTTP_400_BAD_REQUEST,
+                        detail=f"Required variable '{var}' not found in compose template"
+                    )
+        elif "required_variables" in update_data:
+            template = tool_type.compose_template
+            if template:
+                for var in update_data["required_variables"]:
+                    placeholder = f"{{{{{var}}}}}"
+                    if placeholder not in template:
+                        raise HTTPException(
+                            status_code=status.HTTP_400_BAD_REQUEST,
+                            detail=f"Required variable '{var}' not found in compose template"
+                        )
     
     for field, value in update_data.items():
         setattr(tool_type, field, value)
@@ -237,12 +467,141 @@ async def update_tool_type(
     return tool_type
 
 
-@router.delete("/{tool_type_id}", status_code=status.HTTP_204_NO_CONTENT)
+class ToolTypeValidateRequest(BaseModel):
+    definition_type: str
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+
+
+@router.post(
+    "/validate",
+    summary="Validate tool type template",
+    description="Validate a compose template or dockerfile syntax before creating a tool type.",
+)
+async def validate_tool_type_template(
+    data: ToolTypeValidateRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Validate a tool type template syntax.
+
+    Args:
+        data: Validation request with definition type and template.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Validation result with success status and any errors.
+    """
+    await _get_user(session, user_id)
+
+    errors = []
+
+    if data.definition_type == "compose":
+        if not data.compose_template:
+            errors.append("Compose template is required")
+        else:
+            try:
+                parsed = yaml.safe_load(data.compose_template)
+                if not isinstance(parsed, dict):
+                    errors.append("Compose template must be a YAML mapping")
+                elif "services" not in parsed:
+                    errors.append("Compose template must contain 'services' key")
+                elif not parsed["services"]:
+                    errors.append("Compose template must define at least one service")
+            except yaml.YAMLError as e:
+                errors.append(f"Invalid YAML: {e}")
+
+    elif data.definition_type == "dockerfile":
+        if not data.dockerfile_template:
+            errors.append("Dockerfile template is required")
+        elif not data.dockerfile_template.strip().startswith("FROM"):
+            errors.append("Dockerfile must start with a FROM instruction")
+
+    else:
+        errors.append("definition_type must be 'compose' or 'dockerfile'")
+
+    return {
+        "valid": len(errors) == 0,
+        "errors": errors,
+    }
+
+
+@router.get(
+    "/{tool_type_id}/validate",
+    summary="Validate tool type",
+    description="Validate the compose template or dockerfile syntax of a tool type.",
+)
+async def validate_tool_type(
+    tool_type_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Validate a tool type's template syntax.
+
+    Args:
+        tool_type_id: UUID of the tool type to validate.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Validation result with success status and any errors.
+    """
+    await _get_user(session, user_id)
+    tool_type = await session.get(ToolType, tool_type_id)
+    if tool_type is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    
+    errors = []
+    
+    if tool_type.definition_type == "compose":
+        if not tool_type.compose_template:
+            errors.append("Compose template is empty")
+        else:
+            try:
+                parsed = yaml.safe_load(tool_type.compose_template)
+                if not isinstance(parsed, dict):
+                    errors.append("Compose template must be a YAML mapping")
+                elif "services" not in parsed:
+                    errors.append("Compose template must contain 'services' key")
+                elif not parsed["services"]:
+                    errors.append("Compose template must define at least one service")
+            except yaml.YAMLError as e:
+                errors.append(f"Invalid YAML: {e}")
+    
+    elif tool_type.definition_type == "dockerfile":
+        if not tool_type.dockerfile_template:
+            errors.append("Dockerfile template is empty")
+        elif not tool_type.dockerfile_template.strip().startswith("FROM"):
+            errors.append("Dockerfile must start with a FROM instruction")
+    
+    return {
+        "valid": len(errors) == 0,
+        "errors": errors,
+    }
+
+
+@router.delete(
+    "/{tool_type_id}",
+    status_code=status.HTTP_204_NO_CONTENT,
+    summary="Delete tool type",
+    description="Delete a custom tool type. Built-in tool types cannot be deleted.",
+)
 async def delete_tool_type(
     tool_type_id: uuid.UUID,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
+    """Delete a tool type.
+
+    Args:
+        tool_type_id: UUID of the tool type to delete.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        None with 204 status code.
+    """
     user = await _get_user(session, user_id)
     await _require_admin(user)
     

apps/api/src/api/user_config.py

@@ -1,40 +1,22 @@
+import logging
 import uuid
-from typing import Annotated
 
-from fastapi import APIRouter, Cookie, Depends, HTTPException, status
+from fastapi import APIRouter, Depends, HTTPException, status
+
+logger = logging.getLogger(__name__)
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
-from typing import Any
 
-from src.auth.jwt_service import decode_access_token
-from src.config import Settings
-from src.database import SessionLocal
+from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models.user import User
 from src.models.user_config import UserConfig
 
 router = APIRouter(prefix="/users/me", tags=["user-config"])
 
 
-async def get_db_session():
-    async with SessionLocal() as session:
-        yield session
-
-
-async def get_current_user_id(
-    access_token: Annotated[str | None, Cookie()] = None,
-) -> uuid.UUID:
-    if not access_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing access token")
-
-    try:
-        claims = decode_access_token(settings=Settings(), token=access_token)
-        return uuid.UUID(str(claims["sub"]))
-    except Exception:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid access token")
-
-
 async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
     user = await session.get(User, user_id)
     if user is None:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
@@ -42,6 +24,15 @@ async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
 
 
 async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
+    """Get or create user config record.
+
+    Args:
+        session: Database session.
+        user_id: UUID of the user.
+
+    Returns:
+        The user's config, creating a new one if it doesn't exist.
+    """
     result = await session.execute(select(UserConfig).where(UserConfig.user_id == user_id))
     config = result.scalar_one_or_none()
     if config is None:
@@ -59,6 +50,7 @@ class UserConfigResponse(BaseModel):
     theme: str = "system"
     git_user_name: str | None = None
     git_user_email: str | None = None
+    last_session_id: str | None = None
 
 
 class UserConfigUpdate(BaseModel):
@@ -66,31 +58,64 @@ class UserConfigUpdate(BaseModel):
     theme: str | None = None
     git_user_name: str | None = None
     git_user_email: str | None = None
+    last_session_id: str | None = None
 
 
-@router.get("/config", response_model=UserConfigResponse)
+@router.get(
+    "/config",
+    response_model=UserConfigResponse,
+    summary="Get user config",
+    description="Get the current user's configuration settings.",
+)
 async def get_user_config(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
+    """Get the current user's configuration.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The user's configuration settings.
+    """
     _user = await _get_user(session, user_id)
     config = await _get_or_create_config(session, user_id)
     return UserConfigResponse.model_validate(config.config)
 
 
-@router.patch("/config", response_model=UserConfigResponse)
+@router.patch(
+    "/config",
+    response_model=UserConfigResponse,
+    summary="Update user config",
+    description="Update the current user's configuration settings.",
+)
 async def update_user_config(
     data: UserConfigUpdate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
+    """Update the current user's configuration.
+
+    Args:
+        data: Configuration update data with optional fields.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated user configuration.
+    """
     _user = await _get_user(session, user_id)
     config = await _get_or_create_config(session, user_id)
 
     # Merge updates
-    update_data = data.model_dump(exclude_unset=True, exclude_none=True)
-    config.config.update(update_data)
+    update_data = data.model_dump(exclude_unset=True)
+    logger.info("Updating user config for user %s: %s", user_id, update_data)
+    # SQLAlchemy JSON doesn't track dict mutations, so we replace the whole dict
+    config.config = {**config.config, **update_data}
 
     await session.commit()
     await session.refresh(config)
+    logger.info("Updated config: %s", config.config)
     return UserConfigResponse.model_validate(config.config)

apps/api/src/api/users.py

@@ -1,14 +1,11 @@
 import uuid
 from pathlib import Path
-from typing import Annotated
 
-from fastapi import APIRouter, Cookie, Depends, HTTPException, UploadFile, status
+from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.jwt_service import decode_access_token
-from src.config import Settings
-from src.database import SessionLocal
+from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models.user import User
 
 router = APIRouter(prefix="/users", tags=["users"])
@@ -19,25 +16,8 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 
 
-async def get_db_session():
-    async with SessionLocal() as session:
-        yield session
-
-
-async def get_current_user_id(
-    access_token: Annotated[str | None, Cookie()] = None,
-) -> uuid.UUID:
-    if not access_token:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing access token")
-
-    try:
-        claims = decode_access_token(settings=Settings(), token=access_token)
-        return uuid.UUID(str(claims["sub"]))
-    except Exception:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid access token")
-
-
 async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
     user = await session.get(User, user_id)
     if user is None:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
@@ -58,20 +38,49 @@ class UserProfileUpdate(BaseModel):
     email: str | None = None
 
 
-@router.get("/me", response_model=UserProfileResponse)
+@router.get(
+    "/me",
+    response_model=UserProfileResponse,
+    summary="Get current user profile",
+    description="Retrieve the profile of the currently authenticated user.",
+)
 async def get_profile(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
+    """Get the current user's profile.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The user's profile information.
+    """
     return await _get_user(session, user_id)
 
 
-@router.put("/me", response_model=UserProfileResponse)
+@router.put(
+    "/me",
+    response_model=UserProfileResponse,
+    summary="Update user profile",
+    description="Update the current user's profile information.",
+)
 async def update_profile(
     data: UserProfileUpdate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
+    """Update the current user's profile.
+
+    Args:
+        data: Profile update data with optional name and email.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated user profile.
+    """
     user = await _get_user(session, user_id)
 
     if data.name is not None:
@@ -89,12 +98,27 @@ async def update_profile(
     return user
 
 
-@router.post("/me/avatar", response_model=UserProfileResponse)
+@router.post(
+    "/me/avatar",
+    response_model=UserProfileResponse,
+    summary="Upload avatar",
+    description="Upload a profile avatar image (PNG or JPG, max 2MB).",
+)
 async def upload_avatar(
     file: UploadFile,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
+    """Upload a profile avatar image.
+
+    Args:
+        file: The image file to upload (PNG or JPG, max 2MB).
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated user profile with new avatar URL.
+    """
     user = await _get_user(session, user_id)
 
     if file.content_type not in ALLOWED_CONTENT_TYPES:

apps/api/src/auth/__init__.py

@@ -1,12 +1,10 @@
 from src.auth.cookies import build_cookie_options
-from src.auth.jwt_service import decode_access_token, mint_access_token
 from src.auth.oidc import build_login_redirect_url
-from src.auth.refresh_store import hash_refresh_token
+from src.auth.session import create_session_cookie, decode_session_cookie
 
 __all__ = [
     "build_cookie_options",
     "build_login_redirect_url",
-    "decode_access_token",
-    "hash_refresh_token",
-    "mint_access_token",
+    "create_session_cookie",
+    "decode_session_cookie",
 ]

apps/api/src/auth/cookies.py

@@ -1,9 +1,10 @@
 from src.config import Settings
 
 
-def build_cookie_options(settings: Settings) -> dict[str, str | bool]:
+def build_cookie_options(settings: Settings) -> dict[str, str | bool | None]:
     return {
         "httponly": True,
         "secure": settings.cookie_secure,
         "samesite": settings.cookie_samesite,
+        "domain": settings.cookie_domain,
     }

apps/api/src/auth/dependencies.py

@@ -0,0 +1,49 @@
+import uuid
+from typing import Annotated
+
+from fastapi import Cookie, Depends, HTTPException, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.session import decode_session_cookie
+from src.config import Settings
+from src.database import SessionLocal
+from src.models.user import User
+
+
+async def get_db_session():
+    async with SessionLocal() as session:
+        yield session
+
+
+async def get_current_user_id(
+    session_cookie: Annotated[str | None, Cookie(alias="session")] = None,
+) -> uuid.UUID:
+    if not session_cookie:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing session")
+
+    settings = Settings()
+    try:
+        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+        return uuid.UUID(str(payload["user_id"]))
+    except ValueError:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid session")
+
+
+async def get_current_user(
+    session_cookie: Annotated[str | None, Cookie(alias="session")] = None,
+    db_session: AsyncSession = Depends(get_db_session),
+) -> User:
+    if not session_cookie:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing session")
+
+    settings = Settings()
+    try:
+        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+        user_id = uuid.UUID(str(payload["user_id"]))
+    except ValueError:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="invalid session")
+
+    user = await db_session.get(User, user_id)
+    if user is None:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
+    return user

apps/api/src/auth/jwt_service.py

@@ -1,27 +0,0 @@
-from datetime import datetime
-
-from jose import jwt  # type: ignore[import-untyped]
-
-from src.config import Settings
-
-
-def mint_access_token(
-    *,
-    settings: Settings,
-    subject: str,
-    email: str,
-    name: str,
-    expires_at: datetime,
-) -> str:
-    payload = {
-        "sub": subject,
-        "email": email,
-        "name": name,
-        "exp": expires_at,
-    }
-    return jwt.encode(payload, settings.jwt_secret, algorithm=settings.jwt_algorithm)
-
-
-def decode_access_token(*, settings: Settings, token: str) -> dict[str, str | int]:
-    claims = jwt.decode(token, settings.jwt_secret, algorithms=[settings.jwt_algorithm])
-    return dict(claims)

apps/api/src/auth/oidc.py

@@ -1,7 +1,7 @@
+from typing import Any
 from urllib.parse import urlencode
 
 import httpx
-from jose import jwt  # type: ignore[import-untyped]
 
 from src.config import Settings
 
@@ -11,7 +11,6 @@ def build_login_redirect_url(
     settings: Settings,
     redirect_uri: str,
     state: str,
-    nonce: str,
 ) -> str:
     query = urlencode(
         {
@@ -20,7 +19,6 @@ def build_login_redirect_url(
             "redirect_uri": redirect_uri,
             "scope": "openid profile email",
             "state": state,
-            "nonce": nonce,
         }
     )
     return f"{settings.resolved_authentik_authorize_url}?{query}"
@@ -51,27 +49,16 @@ async def exchange_code_for_tokens(
     }
 
 
-async def fetch_jwks(*, settings: Settings, client: httpx.AsyncClient) -> dict[str, list[dict[str, str]]]:
-    response = await client.get(settings.resolved_authentik_jwks_url)
-    response.raise_for_status()
-    payload = response.json()
-    return {"keys": payload["keys"]}
-
-
-def verify_provider_access_token(
+async def fetch_user_info(
     *,
     settings: Settings,
-    token: str,
-    jwks: dict[str, list[dict[str, str]]],
-) -> dict[str, str | int]:
-    unverified_header = jwt.get_unverified_header(token)
-    key_id = unverified_header["kid"]
-    jwk_key = next(key for key in jwks["keys"] if key.get("kid") == key_id)
-    claims = jwt.decode(
-        token,
-        jwk_key,
-        algorithms=[jwk_key.get("alg", "HS256")],
-        audience=settings.authentik_audience,
-        issuer=settings.resolved_authentik_issuer,
+    access_token: str,
+    client: httpx.AsyncClient,
+) -> dict[str, Any]:
+    """Fetch user info from Authentik userinfo endpoint."""
+    response = await client.get(
+        f"{settings.authentik_base_url}/application/o/userinfo/",
+        headers={"Authorization": f"Bearer {access_token}"},
     )
-    return dict(claims)
+    response.raise_for_status()
+    return response.json()

apps/api/src/auth/refresh_store.py

@@ -1,79 +0,0 @@
-from datetime import UTC, datetime
-from hashlib import sha256
-from secrets import token_urlsafe
-
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.refresh_token import RefreshToken
-
-
-def hash_refresh_token(raw_token: str) -> str:
-    return sha256(raw_token.encode("utf-8")).hexdigest()
-
-
-async def create_refresh_token(
-    *,
-    session: AsyncSession,
-    user_id: object,
-    expires_at: datetime,
-    user_agent: str | None,
-    ip_address: str | None,
-) -> tuple[str, RefreshToken]:
-    raw_token = token_urlsafe(48)
-    record = RefreshToken(
-        user_id=user_id,
-        token_hash=hash_refresh_token(raw_token),
-        expires_at=expires_at,
-        created_at=datetime.now(UTC),
-        user_agent=user_agent,
-        ip_address=ip_address,
-    )
-    session.add(record)
-    await session.commit()
-    await session.refresh(record)
-    return raw_token, record
-
-
-async def rotate_refresh_token(
-    *,
-    session: AsyncSession,
-    raw_token: str,
-    user_agent: str | None,
-    ip_address: str | None,
-) -> tuple[str, RefreshToken]:
-    existing_hash = hash_refresh_token(raw_token)
-    existing = await session.scalar(
-        select(RefreshToken).where(
-            RefreshToken.token_hash == existing_hash,
-            RefreshToken.revoked_at.is_(None),
-        )
-    )
-    if existing is None:
-        raise ValueError("refresh token not found")
-    if existing.expires_at <= datetime.now(UTC):
-        raise ValueError("refresh token expired")
-
-    existing.revoked_at = datetime.now(UTC)
-    await session.flush()
-
-    return await create_refresh_token(
-        session=session,
-        user_id=existing.user_id,
-        expires_at=existing.expires_at,
-        user_agent=user_agent,
-        ip_address=ip_address,
-    )
-
-
-async def revoke_refresh_token(*, session: AsyncSession, raw_token: str) -> bool:
-    token_hash = hash_refresh_token(raw_token)
-    existing = await session.scalar(select(RefreshToken).where(RefreshToken.token_hash == token_hash))
-    if existing is None:
-        return False
-    if existing.revoked_at is not None:
-        return True
-
-    existing.revoked_at = datetime.now(UTC)
-    await session.commit()
-    return True

apps/api/src/auth/session.py

@@ -0,0 +1,71 @@
+import hmac
+import hashlib
+import json
+import base64
+from datetime import UTC, datetime, timedelta
+from typing import Any
+
+from src.config import Settings
+
+
+def _base64url_encode(data: bytes) -> str:
+    return base64.urlsafe_b64encode(data).rstrip(b"=").decode("ascii")
+
+
+def _base64url_decode(data: str) -> bytes:
+    padding = 4 - len(data) % 4
+    if padding != 4:
+        data += "=" * padding
+    return base64.urlsafe_b64decode(data)
+
+
+def create_session_cookie(*, settings: Settings, user_id: str) -> str:
+    """Create a signed session cookie value."""
+    payload = {
+        "user_id": user_id,
+        "exp": int((datetime.now(UTC) + timedelta(hours=settings.session_ttl_hours)).timestamp()),
+    }
+    
+    header = _base64url_encode(json.dumps({"alg": "HS256", "typ": "session"}).encode())
+    payload_encoded = _base64url_encode(json.dumps(payload).encode())
+    message = f"{header}.{payload_encoded}"
+    
+    signature = hmac.new(
+        settings.session_secret.encode(),
+        message.encode(),
+        hashlib.sha256,
+    ).digest()
+    signature_encoded = _base64url_encode(signature)
+    
+    return f"{message}.{signature_encoded}"
+
+
+def decode_session_cookie(*, settings: Settings, cookie_value: str) -> dict[str, Any]:
+    """Decode and verify a session cookie. Returns payload or raises ValueError."""
+    parts = cookie_value.split(".")
+    if len(parts) != 3:
+        raise ValueError("invalid session format")
+    
+    header, payload_encoded, signature_encoded = parts
+    message = f"{header}.{payload_encoded}"
+    
+    # Verify signature
+    expected_signature = hmac.new(
+        settings.session_secret.encode(),
+        message.encode(),
+        hashlib.sha256,
+    ).digest()
+    expected_signature_encoded = _base64url_encode(expected_signature)
+    
+    if not hmac.compare_digest(signature_encoded, expected_signature_encoded):
+        raise ValueError("invalid session signature")
+    
+    # Decode payload
+    payload_bytes = _base64url_decode(payload_encoded)
+    payload = json.loads(payload_bytes)
+    
+    # Check expiry
+    if payload.get("exp", 0) < int(datetime.now(UTC).timestamp()):
+        raise ValueError("session expired")
+    
+    return payload

apps/api/src/config.py

@@ -43,13 +43,17 @@ class Settings(BaseSettings):
     authentik_issuer: str | None = None
     authentik_audience: str = "headquarter-web"
 
-    jwt_secret: str = "change-me-jwt-secret"
-    jwt_algorithm: str = "HS256"
-    access_token_ttl_minutes: int = 15
-    refresh_token_ttl_days: int = 7
+    # Session configuration
+    session_secret: str = "change-me-session-secret"
+    session_ttl_hours: int = 24
 
     # Repository storage
     repo_base_path: str = "/data/repos"
+    
+    # Tool instance storage
+    instance_base_path: str = "/data/instances"
+
+
 
     model_config = SettingsConfigDict(env_file=".env", extra="ignore", populate_by_name=True)
 
@@ -118,6 +122,22 @@ class Settings(BaseSettings):
     @property
     def cookie_samesite(self) -> str:
         if self.app_env == "production":
-            return "strict"
+            return "none"
 
         return "lax"
+
+    @property
+    def cookie_domain(self) -> str | None:
+        """Return the parent domain for cross-subdomain cookies.
+
+        E.g., api.example.com and app.example.com both share .example.com
+        """
+        if self.app_env != "production":
+            return None
+
+        # Extract parent domain from api_domain
+        # e.g., "api.headquarter.commumedia.org" -> ".headquarter.commumedia.org"
+        parts = self.api_domain.split(".")
+        if len(parts) >= 3:
+            return "." + ".".join(parts[1:])
+        return None

apps/api/src/database.py

@@ -1,9 +1,7 @@
 import asyncio
 import logging
+import subprocess
 
-from alembic import command
-from alembic.config import Config
-from alembic.runtime.migration import MigrationContext
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
 from sqlalchemy.pool import NullPool
 
@@ -31,12 +29,11 @@ SessionLocal = async_sessionmaker(engine, class_=AsyncSession, expire_on_commit=
 async def init_database(
     max_retries: int = 5,
     retry_delay: float = 2.0,
-    alembic_ini_path: str = "alembic.ini",
 ) -> bool:
     """Initialize the database by running pending migrations.
 
-    Retries the connection with exponential backoff to handle
-    database startup latency in containerized environments.
+    Uses subprocess to run 'alembic upgrade head' to avoid
+    async/sync context manager issues with SQLAlchemy 2.0.
 
     Returns True if migrations succeeded, False otherwise.
     """
@@ -44,42 +41,38 @@ async def init_database(
         try:
             # Test basic connectivity
             from sqlalchemy import text
-            conn = await engine.connect()
+            test_conn = await engine.connect()
             try:
-                await conn.execute(text("SELECT 1"))
+                await test_conn.execute(text("SELECT 1"))
             finally:
-                await conn.close()
+                await test_conn.close()
 
             logger.info("Database connection established.")
 
-            # Check if migrations are already complete
-            def _check_migrations():
-                alembic_cfg = Config(alembic_ini_path)
-                script = command.ScriptDirectory.from_config(alembic_cfg)
-                with engine.connect() as conn:
-                    context = MigrationContext.configure(conn)
-                    current_rev = context.get_current_revision()
-                    head_rev = script.get_current_head()
-                    return current_rev == head_rev, current_rev, head_rev
-
-            is_current, current_rev, head_rev = await asyncio.get_event_loop().run_in_executor(
-                None, _check_migrations
+            # Run migrations via subprocess
+            logger.info("Running database migrations...")
+            result = await asyncio.get_event_loop().run_in_executor(
+                None,
+                lambda: subprocess.run(
+                    ["alembic", "upgrade", "head"],
+                    capture_output=True,
+                    text=True,
+                    cwd="/app",
+                ),
             )
 
-            if is_current:
-                logger.info("Database is already at the latest migration (%s).", head_rev)
+            if result.returncode == 0:
+                logger.info("Database migrations completed successfully.")
+                logger.debug("Alembic output: %s", result.stdout)
                 return True
-
-            logger.info("Current revision: %s, Head revision: %s. Running migrations...", current_rev, head_rev)
-
-            # Run alembic migrations (sync call in executor)
-            def _run_migrations():
-                alembic_cfg = Config(alembic_ini_path)
-                command.upgrade(alembic_cfg, "head")
-
-            await asyncio.get_event_loop().run_in_executor(None, _run_migrations)
-            logger.info("Database migrations completed successfully.")
-            return True
+            else:
+                logger.error("Migration failed: %s", result.stderr)
+                if attempt < max_retries:
+                    wait = retry_delay * (2 ** (attempt - 1))
+                    logger.info("Retrying in %.1f seconds...", wait)
+                    await asyncio.sleep(wait)
+                else:
+                    return False
 
         except Exception as exc:
             error_msg = str(exc).lower()

apps/api/src/main.py

@@ -1,17 +1,30 @@
+import json
 import logging
 import os
 
-from fastapi import FastAPI
+from fastapi import FastAPI, Request
+from fastapi.exceptions import RequestValidationError
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
 from sqlalchemy import select, text
 
 from src.api.auth import router as auth_router
+from src.api.dashboard import router as dashboard_router
 from src.api.git_repositories import router as git_repositories_router
+from src.api.health import router as health_router
 from src.api.projects import router as projects_router
 from src.api.ssh_keys import router as ssh_keys_router
+from src.api.terminal import router as terminal_router
+from src.api.instance_proxy import router as instance_proxy_router
+from src.api.config_folders import router as config_folders_router
+from src.api.tool_configs import router as tool_configs_router
+from src.api.tool_instances import router as tool_instances_router
+from src.api.tool_instances import sessions_router
 from src.api.tool_types import router as tool_types_router
 from src.api.user_config import router as user_config_router
 from src.api.users import router as users_router
+from src.config import Settings
 from src.database import SessionLocal, init_database
 from src.logging_config import (
     ExceptionLoggingMiddleware,
@@ -25,11 +38,71 @@ log_level = os.getenv("LOG_LEVEL", "INFO").upper()
 configure_logging(level=getattr(logging, log_level, logging.INFO))
 
 logger = logging.getLogger(__name__)
+settings = Settings()
 app = FastAPI(title="Headquarter API")
+
+# Configure CORS - must be before other middleware
+# Build allowed origins list including web and api domains
+cors_origins = [settings.web_base_url]
+if settings.api_base_url != settings.web_base_url:
+    cors_origins.append(settings.api_base_url)
+logger.info("CORS configured with origins: %s", cors_origins)
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=cors_origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
 app.add_middleware(RequestLoggingMiddleware)
 app.add_middleware(ExceptionLoggingMiddleware)
 
 
+def _sanitize_validation_errors(errors):
+    """Convert validation errors to JSON-safe format."""
+    sanitized = []
+    for error in errors:
+        safe_error = {
+            "type": error.get("type"),
+            "loc": error.get("loc"),
+            "msg": error.get("msg"),
+            "input": str(error.get("input")) if error.get("input") is not None else None,
+        }
+        # Convert ctx to safe format
+        ctx = error.get("ctx")
+        if ctx:
+            safe_ctx = {}
+            for key, value in ctx.items():
+                if isinstance(value, Exception):
+                    safe_ctx[key] = str(value)
+                elif isinstance(value, (str, int, float, bool, type(None))):
+                    safe_ctx[key] = value
+                else:
+                    safe_ctx[key] = str(value)
+            safe_error["ctx"] = safe_ctx
+        sanitized.append(safe_error)
+    return sanitized
+
+
+@app.exception_handler(RequestValidationError)
+async def validation_exception_handler(request: Request, exc: RequestValidationError):
+    """Log validation errors and return detailed response."""
+    errors = exc.errors()
+    logger.warning(
+        "Validation error for %s %s: %s",
+        request.method,
+        request.url.path,
+        errors,
+    )
+    safe_errors = _sanitize_validation_errors(errors)
+    return JSONResponse(
+        status_code=422,
+        content={"detail": safe_errors},
+    )
+
+
 async def _table_exists(session, table_name: str) -> bool:
     """Check if a table exists in the database."""
     try:
@@ -63,6 +136,8 @@ async def seed_builtin_tool_types():
                 "name": "code-server",
                 "display_name": "VS Code Server",
                 "description": "VS Code running in the browser via code-server",
+                "category": "editor",
+                "interfaces": ["web"],
                 "compose_template": """version: "3.8"
 services:
   code-server:
@@ -77,12 +152,16 @@ services:
     ports:
       - "8443:8443"
     restart: unless-stopped""",
+                "default_port": 8443,
                 "required_variables": ["REPO_PATH", "TOOL_NAME"],
             },
             {
                 "name": "jupyter-notebook",
                 "display_name": "Jupyter Notebook",
                 "description": "Jupyter Lab for interactive development",
+                "category": "notebook",
+                "interfaces": ["web"],
+                "default_port": 8888,
                 "compose_template": """version: "3.8"
 services:
   jupyter:
@@ -97,6 +176,47 @@ services:
     restart: unless-stopped""",
                 "required_variables": ["REPO_PATH", "TOOL_NAME"],
             },
+            {
+                "name": "opencode",
+                "display_name": "OpenCode",
+                "description": "AI coding assistant - run opencode in terminal",
+                "category": "ai-assistant",
+                "interfaces": ["terminal"],
+                "default_port": 3000,
+                "compose_template": """version: "3.8"
+services:
+  opencode:
+    image: node:20-slim
+    container_name: {{TOOL_NAME}}
+    working_dir: /workspace
+    environment:
+      - HOME=/tmp
+    volumes:
+      - {{REPO_PATH}}:/workspace
+      - opencode_home:/tmp
+    ports:
+      - "3000:3000"
+    command: >
+      sh -c "set -x &&
+             apt-get update && apt-get install -y git ca-certificates &&
+             echo 'Installing opencode...' &&
+             npm install -g opencode-ai 2>&1 || echo 'ERROR: npm install failed' &&
+             which opencode || echo 'ERROR: opencode not in PATH' &&
+             npm bin -g &&
+             ls -la $(npm bin -g) || echo 'ERROR: global bin dir not found' &&
+             echo 'export PATH=\"$(npm bin -g):\$PATH\"' >> /root/.bashrc &&
+             echo 'cd /workspace' >> /root/.bashrc &&
+             echo 'OpenCode installation complete' &&
+             cd /workspace &&
+             exec tail -f /dev/null"
+    stdin_open: true
+    tty: true
+    restart: unless-stopped
+
+volumes:
+  opencode_home:""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
         ]
 
         for tool_data in builtin_types:
@@ -106,11 +226,27 @@ services:
                     name=tool_data["name"],
                     display_name=tool_data["display_name"],
                     description=tool_data["description"],
+                    category=tool_data["category"],
+                    interfaces=tool_data["interfaces"],
+                    definition_type="compose",
                     compose_template=tool_data["compose_template"],
                     required_variables=tool_data["required_variables"],
+                    default_port=tool_data.get("default_port"),
                     is_builtin=True,
                 )
                 session.add(tool_type)
+                logger.info("Created built-in tool type: %s", tool_data["name"])
+            else:
+                # Update existing built-in tool types to reflect code changes
+                existing.display_name = tool_data["display_name"]
+                existing.description = tool_data["description"]
+                existing.category = tool_data["category"]
+                existing.interfaces = tool_data["interfaces"]
+                existing.definition_type = "compose"
+                existing.compose_template = tool_data["compose_template"]
+                existing.required_variables = tool_data["required_variables"]
+                existing.default_port = tool_data.get("default_port")
+                logger.info("Updated built-in tool type: %s", tool_data["name"])
 
         await session.commit()
         logger.info("Built-in tool types seeded successfully.")
@@ -123,22 +259,27 @@ async def on_startup():
     # Initialize database (run migrations)
     db_ready = await init_database()
     if not db_ready:
-        logger.error("Database initialization failed. API may not function correctly.")
-        # Continue anyway so the health endpoint remains available
+        logger.error("Database initialization failed. Shutting down.")
+        import sys
+        sys.exit(1)
 
     # Seed built-in data
     await seed_builtin_tool_types()
     logger.info("Startup complete.")
 
-@app.get("/health")
-async def health_check():
-    return {"status": "healthy"}
-
+app.include_router(health_router)
 app.include_router(auth_router)
+app.include_router(dashboard_router)
 app.include_router(projects_router)
 app.include_router(users_router)
 app.include_router(ssh_keys_router)
 app.include_router(git_repositories_router)
 app.include_router(user_config_router)
 app.include_router(tool_types_router)
+app.include_router(config_folders_router)
+app.include_router(tool_instances_router)
+app.include_router(tool_configs_router)
+app.include_router(sessions_router)
+app.include_router(instance_proxy_router)
+app.include_router(terminal_router)
 app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")

apps/api/src/models/__init__.py

@@ -1,10 +1,27 @@
 from src.models.base import Base
+from src.models.config_folder import ConfigFolder
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
 from src.models.git_repository import GitRepository
 from src.models.project import Project
-from src.models.refresh_token import RefreshToken
 from src.models.ssh_key import SSHKey
+from src.models.tool_instance import ToolInstance
 from src.models.tool_type import ToolType
 from src.models.user import User
 from src.models.user_config import UserConfig
 
-__all__ = ["Base", "GitRepository", "Project", "RefreshToken", "SSHKey", "ToolType", "User", "UserConfig"]
+__all__ = [
+    "Base",
+    "ConfigFolder",
+    "ConfigInclude",
+    "ConfigMount",
+    "ConfigProfile",
+    "GitRepository",
+    "Project",
+    "SSHKey",
+    "ToolInstance",
+    "ToolType",
+    "User",
+    "UserConfig",
+]

apps/api/src/models/config_folder.py

@@ -0,0 +1,33 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.user import User
+
+
+class ConfigFolder(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_folders"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
+    )
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+    mount_path: Mapped[str] = mapped_column(String(1024), nullable=False)
+    files: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"relative/path": "content", ...}
+    project_overrides: Mapped[dict | None] = mapped_column(
+        JSON, default=dict, nullable=True
+    )  # {"project_id": {"mount_path": "...", "files": {...}}}
+    # DEPRECATED: Legacy auto-mounting flag. No longer used for launch-time
+    # auto-mounting. Use ConfigProfile and ToolInstance.selected_profile_id instead.
+    is_active: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
+
+    user: Mapped["User"] = relationship()

apps/api/src/models/config_include.py

@@ -0,0 +1,36 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, Integer, UniqueConstraint
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.config_profile import ConfigProfile
+
+
+class ConfigInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_includes"
+    __table_args__ = (
+        UniqueConstraint("profile_id", "included_profile_id", name="uq_config_includes_pair"),
+    )
+
+    profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    included_profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
+
+    profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[profile_id],
+        back_populates="includes",
+    )
+    included_profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[included_profile_id],
+    )

apps/api/src/models/config_mount.py

@@ -0,0 +1,35 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, Integer, String, Text
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.config_profile import ConfigProfile
+
+
+class ConfigMount(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_mounts"
+
+    profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    mount_path: Mapped[str] = mapped_column(String(1024), nullable=False)
+    content: Mapped[str | None] = mapped_column(Text, nullable=True)
+    source_profile_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
+    )
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
+
+    profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[profile_id],
+        back_populates="mounts",
+    )
+    source_profile: Mapped["ConfigProfile | None"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[source_profile_id],
+    )

apps/api/src/models/config_profile.py

@@ -0,0 +1,39 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, String, Text, UniqueConstraint
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.user import User
+
+
+class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_profiles"
+    __table_args__ = (
+        UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
+    )
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+
+    user: Mapped["User"] = relationship()
+    includes: Mapped[list["ConfigInclude"]] = relationship(
+        "ConfigInclude",
+        foreign_keys="ConfigInclude.profile_id",
+        back_populates="profile",
+        cascade="all, delete-orphan",
+        order_by="ConfigInclude.order_index",
+    )
+    mounts: Mapped[list["ConfigMount"]] = relationship(
+        "ConfigMount",
+        back_populates="profile",
+        cascade="all, delete-orphan",
+        order_by="ConfigMount.order_index",
+    )

apps/api/src/models/refresh_token.py

@@ -1,24 +0,0 @@
-from datetime import datetime
-from typing import TYPE_CHECKING
-
-from sqlalchemy import DateTime, ForeignKey, String
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.user import User
-
-
-class RefreshToken(UUIDPrimaryKeyMixin, Base):
-    __tablename__ = "refresh_tokens"
-
-    user_id: Mapped[str] = mapped_column(ForeignKey("users.id"), nullable=False, index=True)
-    token_hash: Mapped[str] = mapped_column(String(255), unique=True, nullable=False)
-    expires_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, index=True)
-    revoked_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
-    user_agent: Mapped[str | None] = mapped_column(String(512), nullable=True)
-    ip_address: Mapped[str | None] = mapped_column(String(64), nullable=True)
-    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False)
-
-    user: Mapped["User"] = relationship(back_populates="refresh_tokens")

apps/api/src/models/ssh_key.py

@@ -5,14 +5,14 @@ from sqlalchemy import ForeignKey, String, Text
 from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from src.models.base import Base, UUIDPrimaryKeyMixin
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
     from src.models.user import User
 
 
-class SSHKey(UUIDPrimaryKeyMixin, Base):
+class SSHKey(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     __tablename__ = "ssh_keys"
 
     name: Mapped[str] = mapped_column(String(255))

apps/api/src/models/tool_config.py

@@ -0,0 +1,48 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, JSON, String, Text
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.project import Project
+    from src.models.tool_type import ToolType
+    from src.models.user import User
+
+
+class ToolConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "tool_configs"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id"), nullable=False
+    )
+    tool_type_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("tool_types.id"), nullable=False
+    )
+    project_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("projects.id"), nullable=True
+    )
+    key: Mapped[str] = mapped_column(String(255), nullable=False)
+    value: Mapped[str] = mapped_column(Text, nullable=False)
+    config_type: Mapped[str] = mapped_column(
+        String(20), nullable=False, default="env"
+    )  # "env" or "file"
+    file_path: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )  # Only for file type
+    port_override: Mapped[int | None] = mapped_column(nullable=True)
+    start_command: Mapped[str | None] = mapped_column(Text, nullable=True)
+    working_directory: Mapped[str | None] = mapped_column(Text, nullable=True)
+    environment_variables: Mapped[dict | None] = mapped_column(
+        JSON, default=dict, nullable=True
+    )
+    volumes: Mapped[list[dict] | None] = mapped_column(
+        JSON, default=list, nullable=True
+    )
+
+    user: Mapped["User"] = relationship()
+    tool_type: Mapped["ToolType"] = relationship()
+    project: Mapped["Project | None"] = relationship()

apps/api/src/models/tool_instance.py

@@ -0,0 +1,74 @@
+import uuid
+from datetime import datetime
+from typing import TYPE_CHECKING
+
+from sqlalchemy import DateTime, ForeignKey, Integer, String
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.config_profile import ConfigProfile
+    from src.models.git_repository import GitRepository
+    from src.models.project import Project
+    from src.models.tool_type import ToolType
+    from src.models.user import User
+
+
+class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "tool_instances"
+
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    display_name: Mapped[str] = mapped_column(String(255), nullable=False)
+    tool_type_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("tool_types.id"), nullable=False
+    )
+    repository_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("git_repositories.id"), nullable=False
+    )
+    project_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("projects.id"), nullable=False
+    )
+    owner_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id"), nullable=False
+    )
+    status: Mapped[str] = mapped_column(
+        String(50), nullable=False, default="pending"
+    )
+    container_id: Mapped[str | None] = mapped_column(
+        String(255), nullable=True
+    )
+    container_name: Mapped[str | None] = mapped_column(
+        String(255), nullable=True
+    )
+    compose_path: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )
+    url: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )
+    public_url: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )
+    tunnel_id: Mapped[str | None] = mapped_column(
+        String(255), nullable=True
+    )
+    port: Mapped[int | None] = mapped_column(
+        Integer, nullable=True
+    )
+    last_started_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True
+    )
+    last_stopped_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True
+    )
+    selected_profile_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
+    )
+
+    tool_type: Mapped["ToolType"] = relationship()
+    repository: Mapped["GitRepository"] = relationship()
+    project: Mapped["Project"] = relationship()
+    owner: Mapped["User"] = relationship()
+    selected_profile: Mapped["ConfigProfile | None"] = relationship()

apps/api/src/models/tool_type.py

@@ -17,7 +17,18 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     name: Mapped[str] = mapped_column(String(255), unique=True, nullable=False)
     display_name: Mapped[str] = mapped_column(String(255), nullable=False)
     description: Mapped[str | None] = mapped_column(Text, nullable=True)
-    compose_template: Mapped[str] = mapped_column(Text, nullable=False)
+    category: Mapped[str] = mapped_column(String(50), nullable=False, default="other")
+    interfaces: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
+    default_port: Mapped[int] = mapped_column(nullable=False)
+    definition_type: Mapped[str] = mapped_column(
+        String(20), nullable=False, default="compose"
+    )  # "compose" or "dockerfile"
+    compose_template: Mapped[str | None] = mapped_column(Text, nullable=True)
+    dockerfile_template: Mapped[str | None] = mapped_column(Text, nullable=True)
+    build_context: Mapped[dict | None] = mapped_column(
+        JSON, default=dict, nullable=True
+    )
+    readiness_probe: Mapped[dict | None] = mapped_column(JSON, nullable=True)
     required_variables: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
     is_builtin: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
     created_by_id: Mapped[uuid.UUID | None] = mapped_column(

apps/api/src/models/user.py

@@ -7,7 +7,6 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.refresh_token import RefreshToken
     from src.models.ssh_key import SSHKey
     from src.models.user_config import UserConfig
 
@@ -21,6 +20,5 @@ class User(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     avatar_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
 
     projects: Mapped[list["Project"]] = relationship(back_populates="owner")
-    refresh_tokens: Mapped[list["RefreshToken"]] = relationship(back_populates="user")
     ssh_keys: Mapped[list["SSHKey"]] = relationship(back_populates="user")
     user_config: Mapped["UserConfig | None"] = relationship(back_populates="user", uselist=False)

apps/api/src/models/user_config.py

@@ -18,3 +18,23 @@ class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     config: Mapped[dict[str, object]] = mapped_column(JSON, default=dict, nullable=False)
 
     user: Mapped["User"] = relationship(back_populates="user_config")
+
+    @property
+    def default_profile_id(self) -> uuid.UUID | None:
+        profile_id = self.config.get("default_profile_id")
+        return uuid.UUID(profile_id) if profile_id else None
+
+    @default_profile_id.setter
+    def default_profile_id(self, value: uuid.UUID | None) -> None:
+        if value is not None:
+            self.config["default_profile_id"] = str(value)
+        elif "default_profile_id" in self.config:
+            del self.config["default_profile_id"]
+
+    @property
+    def default_profiles(self) -> dict[str, str]:
+        return self.config.get("default_profiles", {})
+
+    @default_profiles.setter
+    def default_profiles(self, value: dict[str, str]) -> None:
+        self.config["default_profiles"] = value

apps/api/src/services/docker.py

@@ -0,0 +1,456 @@
+"""Docker service for managing tool instances."""
+
+import os
+import subprocess
+from pathlib import Path
+from typing import Any
+
+
+def render_compose_template(template: str, variables: dict[str, Any]) -> str:
+    """Render a Docker Compose template with variable substitution.
+
+    Args:
+        template: The compose template string
+        variables: Dictionary of variable names to values
+
+    Returns:
+        Rendered compose file content
+    """
+    result = template
+    for key, value in variables.items():
+        placeholder = f"{{{{{key}}}}}"
+        result = result.replace(placeholder, str(value))
+    return result
+
+
+def ensure_instance_directory(instance_id: str, base_path: str | None = None) -> str:
+    """Create and return the instance directory path.
+
+    Args:
+        instance_id: Unique instance identifier
+        base_path: Base directory for all instances (defaults to Settings.instance_base_path)
+
+    Returns:
+        Absolute path to instance directory
+    """
+    if base_path is None:
+        from src.config import Settings
+        base_path = Settings().instance_base_path
+    instance_dir = Path(base_path) / instance_id
+    instance_dir.mkdir(parents=True, exist_ok=True)
+    return str(instance_dir.absolute())
+
+
+def write_compose_file(instance_dir: str, content: str) -> str:
+    """Write the rendered compose file to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        content: Rendered compose content
+
+    Returns:
+        Path to the compose file
+    """
+    compose_path = Path(instance_dir) / "docker-compose.yml"
+    compose_path.write_text(content)
+    return str(compose_path)
+
+
+def write_env_file(instance_dir: str, env_vars: dict[str, str]) -> str:
+    """Write environment variables to a .env file.
+
+    Args:
+        instance_dir: Path to instance directory
+        env_vars: Dictionary of env var names to values
+
+    Returns:
+        Path to the env file
+    """
+    env_path = Path(instance_dir) / ".env"
+    lines = [f'{key}="{value}"' for key, value in env_vars.items()]
+    env_path.write_text("\n".join(lines) + "\n")
+    return str(env_path)
+
+
+def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
+    """Write config files to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        files: Dictionary of file paths (relative to instance dir) to content
+    """
+    instance_path = Path(instance_dir)
+    for file_path, content in files.items():
+        # Ensure the path is within the instance directory (security)
+        full_path = instance_path / file_path
+        try:
+            full_path.resolve().relative_to(instance_path.resolve())
+        except ValueError:
+            raise ValueError(f"File path '{file_path}' escapes instance directory")
+        
+        full_path.parent.mkdir(parents=True, exist_ok=True)
+        full_path.write_text(content)
+
+
+def write_config_folder_files(instance_dir: str, folders: list, project_id: str | None = None) -> list[dict]:
+    """Write config folder files to the instance directory and return volume mounts.
+
+    Args:
+        instance_dir: Path to instance directory
+        folders: List of ConfigFolder objects
+        project_id: Optional project ID for applying overrides
+
+    Returns:
+        List of volume mount dicts [{"source": "...", "target": "...", "type": "..."}]
+    """
+    instance_path = Path(instance_dir)
+    volume_mounts = []
+
+    for folder in folders:
+        # Determine mount path (with project override if applicable)
+        mount_path = folder.mount_path
+        files = folder.files.copy()
+        
+        if project_id and folder.project_overrides:
+            override = folder.project_overrides.get(str(project_id))
+            if override:
+                if override.get("mount_path"):
+                    mount_path = override["mount_path"]
+                if override.get("files"):
+                    files.update(override["files"])
+        
+        # Write files to instance directory
+        folder_dir = instance_path / "volumes" / folder.name
+        folder_dir.mkdir(parents=True, exist_ok=True)
+        
+        for file_path, content in files.items():
+            # Security: ensure path doesn't escape folder_dir
+            full_path = folder_dir / file_path
+            try:
+                full_path.resolve().relative_to(folder_dir.resolve())
+            except ValueError:
+                logger.warning("Config folder file path escapes directory: %s", file_path)
+                continue
+            
+            full_path.parent.mkdir(parents=True, exist_ok=True)
+            full_path.write_text(content)
+        
+        # Add volume mount
+        volume_mounts.append({
+            "source": str(folder_dir),
+            "target": mount_path,
+            "type": "bind",
+        })
+    
+    return volume_mounts
+
+
+def execute_compose_command(
+    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
+) -> tuple[int, str, str]:
+    """Execute a docker compose command.
+
+    Args:
+        compose_path: Path to docker-compose.yml
+        action: The compose action (up, down, start, stop, restart)
+        timeout: Command timeout in seconds
+        env_file: Optional path to .env file for environment variables
+
+    Returns:
+        Tuple of (returncode, stdout, stderr)
+    """
+    instance_dir = Path(compose_path).parent
+
+    cmd = ["docker", "compose", "-f", compose_path]
+    
+    if env_file:
+        cmd.extend(["--env-file", env_file])
+
+    if action == "up":
+        cmd.extend(["up", "-d"])
+    elif action == "down":
+        cmd.extend(["down", "-v"])
+    elif action in ("start", "stop", "restart"):
+        cmd.append(action)
+    else:
+        raise ValueError(f"Unknown compose action: {action}")
+
+    result = subprocess.run(
+        cmd,
+        cwd=str(instance_dir),
+        capture_output=True,
+        text=True,
+        timeout=timeout,
+    )
+
+    return result.returncode, result.stdout, result.stderr
+
+
+def get_container_id(instance_name: str) -> str | None:
+    """Get the container ID for a compose service.
+
+    Args:
+        instance_name: The service name in compose
+
+    Returns:
+        Container ID or None if not found
+    """
+    result = subprocess.run(
+        ["docker", "ps", "-q", "--filter", f"name={instance_name}"],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0 and result.stdout.strip():
+        return result.stdout.strip().split("\n")[0]
+    return None
+
+
+def get_container_name(instance_name: str) -> str | None:
+    """Get the full container name for a compose service.
+
+    Args:
+        instance_name: The service name in compose
+
+    Returns:
+        Container name or None if not found
+    """
+    result = subprocess.run(
+        ["docker", "ps", "--format", "{{.Names}}", "--filter", f"name={instance_name}"],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0 and result.stdout.strip():
+        return result.stdout.strip().split("\n")[0]
+    return None
+
+
+def connect_container_to_network(container_name: str, network_name: str = "backend") -> bool:
+    """Connect a Docker container to an existing network.
+
+    Args:
+        container_name: Name or ID of the container
+        network_name: Name of the Docker network (default: backend)
+
+    Returns:
+        True if successful, False otherwise
+    """
+    result = subprocess.run(
+        ["docker", "network", "connect", network_name, container_name],
+        capture_output=True,
+        text=True,
+    )
+    return result.returncode == 0
+
+
+def get_container_status(container_id: str) -> str:
+    """Get the status of a Docker container.
+
+    Args:
+        container_id: Docker container ID
+
+    Returns:
+        Container status string (running, exited, etc.)
+    """
+    result = subprocess.run(
+        ["docker", "inspect", "-f", "{{.State.Status}}", container_id],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0:
+        return result.stdout.strip()
+    return "unknown"
+
+
+def get_container_logs(container_id: str, tail: int = 100) -> str:
+    """Get the logs of a Docker container.
+
+    Args:
+        container_id: Docker container ID
+        tail: Number of lines to return
+
+    Returns:
+        Container logs
+    """
+    result = subprocess.run(
+        ["docker", "logs", "--tail", str(tail), container_id],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0:
+        return result.stdout
+    return f"Failed to get logs: {result.stderr}"
+
+
+def find_free_port(start: int = 10000, end: int = 20000) -> int:
+    """Find a free TCP port in the given range.
+
+    Args:
+        start: Start of port range
+        end: End of port range
+
+    Returns:
+        Free port number
+    """
+    import socket
+
+    for port in range(start, end):
+        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+            if s.connect_ex(("localhost", port)) != 0:
+                return port
+
+    raise RuntimeError(f"No free port found in range {start}-{end}")
+
+
+import subprocess
+import time
+import re
+
+
+def start_cloudflared_tunnel(
+    container_name: str, port: int, timeout: int = 30
+) -> dict[str, str]:
+    """Start a temporary Cloudflare tunnel for a container.
+
+    Uses 'cloudflared tunnel --url' to create a temporary tunnel
+    with a random trycloudflare.com URL.
+
+    Args:
+        container_name: Name of the Docker container to tunnel to
+        port: Port number the container listens on
+        timeout: Maximum seconds to wait for tunnel URL
+
+    Returns:
+        Dict with 'url' (the public tunnel URL) and 'pid' (process ID)
+    """
+    import subprocess
+    import time
+    import re
+    import logging
+
+    logger = logging.getLogger(__name__)
+
+    # First verify the container is accessible
+    logger.info("Checking connectivity to %s:%d...", container_name, port)
+    for attempt in range(10):
+        check = subprocess.run(
+            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}", 
+             f"http://{container_name}:{port}"],
+            capture_output=True,
+            text=True,
+            timeout=5,
+        )
+        logger.info("Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip())
+        if check.returncode == 0:
+            break
+        time.sleep(1)
+    else:
+        logger.warning("Container %s:%d not responding to curl checks", container_name, port)
+
+    # Run cloudflared in background, capture output
+    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
+    proc = subprocess.Popen(
+        ["cloudflared", "tunnel", "--url", f"http://{container_name}:{port}"],
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        text=True,
+    )
+
+    # Wait for the URL to appear in output
+    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
+    start_time = time.time()
+    url = None
+
+    while time.time() - start_time < timeout:
+        # Read available output
+        import select
+        readable, _, _ = select.select([proc.stdout], [], [], 1.0)
+        if readable:
+            line = proc.stdout.readline()
+            if line:
+                match = url_pattern.search(line)
+                if match:
+                    url = match.group(0)
+                    break
+
+    if not url:
+        proc.terminate()
+        proc.wait(timeout=5)
+        raise RuntimeError(
+            f"Failed to get tunnel URL within {timeout}s. "
+            f"cloudflared output may contain errors."
+        )
+
+    return {"url": url, "pid": str(proc.pid)}
+
+
+def stop_cloudflared_tunnel(pid: str) -> None:
+    """Stop a cloudflared tunnel process.
+
+    Args:
+        pid: Process ID of the cloudflared tunnel
+    """
+    import os
+    import signal
+
+    try:
+        os.kill(int(pid), signal.SIGTERM)
+    except ProcessLookupError:
+        pass  # Already stopped
+
+
+def recreate_tunnel(
+    container_name: str, port: int, old_pid: str | None = None
+) -> dict[str, str]:
+    """Recreate a temporary Cloudflare tunnel.
+
+    Stops the old tunnel (if pid provided) and starts a new one.
+
+    Args:
+        container_name: Name of the Docker container to tunnel to
+        port: Port number the container listens on
+        old_pid: Optional PID of the old tunnel process to stop
+
+    Returns:
+        Dict with 'url' and 'pid' for the new tunnel
+    """
+    if old_pid:
+        stop_cloudflared_tunnel(old_pid)
+
+    return start_cloudflared_tunnel(container_name, port)
+
+
+def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
+    """Check if a tunnel URL is healthy.
+
+    Args:
+        url: The tunnel URL to check
+        timeout: Request timeout in seconds
+
+    Returns:
+        Dict with 'healthy' (bool) and 'status_code' (int or None)
+    """
+    import subprocess
+
+    try:
+        result = subprocess.run(
+            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}",
+             "--max-time", str(timeout), url],
+            capture_output=True,
+            text=True,
+            timeout=timeout + 5,
+        )
+        status_code = int(result.stdout.strip())
+        return {
+            "healthy": 200 <= status_code < 400,
+            "status_code": status_code,
+        }
+    except (ValueError, subprocess.TimeoutExpired, Exception) as e:
+        return {
+            "healthy": False,
+            "status_code": None,
+            "error": str(e),
+        }

apps/api/src/services/docker_build.py

@@ -0,0 +1,69 @@
+"""Docker build service for building images from Dockerfiles."""
+
+import logging
+import subprocess
+
+logger = logging.getLogger(__name__)
+
+
+def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dict | None = None) -> tuple[int, str, str]:
+    """Build a Docker image from a Dockerfile.
+
+    Args:
+        instance_dir: Directory containing the Dockerfile
+        dockerfile: Dockerfile content
+        tag: Image tag to apply
+        build_context: Optional build context files {path: content}
+
+    Returns:
+        Tuple of (returncode, stdout, stderr)
+    """
+    import os
+    from pathlib import Path
+
+    # Write Dockerfile
+    dockerfile_path = Path(instance_dir) / "Dockerfile"
+    dockerfile_path.write_text(dockerfile)
+    logger.info("Wrote Dockerfile to %s", dockerfile_path)
+
+    # Write build context files
+    if build_context:
+        for file_path, content in build_context.items():
+            full_path = Path(instance_dir) / file_path
+            # Security: ensure path doesn't escape instance_dir
+            try:
+                full_path.resolve().relative_to(Path(instance_dir).resolve())
+            except ValueError:
+                logger.error("Build context file path escapes instance directory: %s", file_path)
+                raise ValueError(f"Build context file path '{file_path}' escapes instance directory")
+            
+            full_path.parent.mkdir(parents=True, exist_ok=True)
+            full_path.write_text(content)
+            logger.info("Wrote build context file: %s", full_path)
+
+    # Build image
+    logger.info("Building Docker image with tag: %s", tag)
+    cmd = [
+        "docker", "build",
+        "-t", tag,
+        "-f", str(dockerfile_path),
+        instance_dir,
+    ]
+
+    try:
+        result = subprocess.run(
+            cmd,
+            capture_output=True,
+            text=True,
+            timeout=300,  # 5 minute timeout for builds
+        )
+        logger.info("Docker build completed: returncode=%d", result.returncode)
+        if result.returncode != 0:
+            logger.error("Docker build failed: %s", result.stderr[:1000])
+        return result.returncode, result.stdout, result.stderr
+    except subprocess.TimeoutExpired:
+        logger.error("Docker build timed out after 300 seconds")
+        return 1, "", "Build timed out after 300 seconds"
+    except Exception as exc:
+        logger.exception("Docker build failed: %s", exc)
+        return 1, "", str(exc)

apps/api/src/services/readiness_probe.py

@@ -0,0 +1,66 @@
+"""Readiness probe service for checking if containers are ready."""
+
+import asyncio
+import logging
+import subprocess
+
+logger = logging.getLogger(__name__)
+
+
+async def execute_probe(
+    container_id: str,
+    command: str,
+    timeout: int = 30,
+    interval: int = 2,
+) -> tuple[bool, list[str]]:
+    """Execute a readiness probe command inside a container.
+
+    Args:
+        container_id: Docker container ID or name
+        command: Command to execute inside the container
+        timeout: Maximum total time to wait (seconds)
+        interval: Time between retries (seconds)
+
+    Returns:
+        Tuple of (success, logs)
+    """
+    logs = []
+    start_time = asyncio.get_event_loop().time()
+    attempt = 0
+
+    while True:
+        attempt += 1
+        elapsed = asyncio.get_event_loop().time() - start_time
+        
+        if elapsed >= timeout:
+            logs.append(f"Probe timed out after {timeout}s ({attempt} attempts)")
+            return False, logs
+
+        try:
+            logger.debug("Probe attempt %d: %s", attempt, command)
+            
+            # Execute command inside container
+            result = subprocess.run(
+                ["docker", "exec", container_id, "sh", "-c", command],
+                capture_output=True,
+                text=True,
+                timeout=interval,  # Each attempt has its own timeout
+            )
+            
+            if result.returncode == 0:
+                logs.append(f"Attempt {attempt}: Success")
+                if result.stdout:
+                    logs.append(f"Output: {result.stdout.strip()}")
+                return True, logs
+            else:
+                logs.append(f"Attempt {attempt}: Failed (exit code {result.returncode})")
+                if result.stderr:
+                    logs.append(f"Stderr: {result.stderr.strip()[:200]}")
+                
+        except subprocess.TimeoutExpired:
+            logs.append(f"Attempt {attempt}: Command timed out")
+        except Exception as exc:
+            logs.append(f"Attempt {attempt}: Error - {exc}")
+
+        # Wait before next attempt
+        await asyncio.sleep(interval)

apps/api/src/services/terminal_manager.py

@@ -0,0 +1,96 @@
+"""Terminal session manager for WebSocket connections."""
+
+import asyncio
+import uuid
+from typing import Any
+
+from fastapi import WebSocket
+
+from src.services.terminal_session import TerminalSession
+
+
+class TerminalManager:
+    """Manages active terminal sessions."""
+
+    def __init__(self) -> None:
+        self._sessions: dict[str, TerminalSession] = {}
+
+    async def create_session(
+        self,
+        instance_id: uuid.UUID,
+        container_id: str,
+        websocket: WebSocket,
+    ) -> TerminalSession:
+        """Create a new terminal session."""
+        session_id = str(uuid.uuid4())
+        session = TerminalSession(session_id, instance_id, container_id)
+        await session.start()
+        self._sessions[session_id] = session
+
+        # Start background tasks for I/O streaming
+        asyncio.create_task(self._read_loop(session, websocket))
+        asyncio.create_task(self._write_loop(session, websocket))
+
+        return session
+
+    async def _read_loop(self, session: TerminalSession, websocket: WebSocket) -> None:
+        """Read output from the container and send to WebSocket."""
+        try:
+            while session.is_alive() and not session._closed:
+                data = await session.read_output()
+                if data:
+                    await websocket.send_bytes(data)
+                else:
+                    await asyncio.sleep(0.01)
+        except Exception:
+            pass
+        finally:
+            await self._cleanup_session(session)
+
+    async def _write_loop(self, session: TerminalSession, websocket: WebSocket) -> None:
+        """Read input from WebSocket and send to container."""
+        try:
+            while session.is_alive() and not session._closed:
+                message = await websocket.receive()
+                if message["type"] == "websocket.receive":
+                    if "bytes" in message:
+                        await session.write_input(message["bytes"])
+                    elif "text" in message:
+                        text = message["text"]
+                        if text.startswith("{"):
+                            # Control message (JSON)
+                            import json
+                            try:
+                                ctrl = json.loads(text)
+                                if ctrl.get("type") == "resize":
+                                    await session.resize(
+                                        ctrl.get("cols", 80),
+                                        ctrl.get("rows", 24),
+                                    )
+                            except json.JSONDecodeError:
+                                pass
+                        else:
+                            await session.write_input(text.encode("utf-8"))
+                elif message["type"] == "websocket.disconnect":
+                    break
+        except Exception:
+            pass
+        finally:
+            await self._cleanup_session(session)
+
+    async def _cleanup_session(self, session: TerminalSession) -> None:
+        """Clean up a session."""
+        if session.session_id in self._sessions:
+            del self._sessions[session.session_id]
+        await session.close()
+
+    async def close_all(self) -> None:
+        """Close all active sessions."""
+        sessions = list(self._sessions.values())
+        self._sessions.clear()
+        for session in sessions:
+            await session.close()
+
+
+# Global terminal manager instance
+terminal_manager = TerminalManager()

apps/api/src/services/terminal_session.py

@@ -0,0 +1,117 @@
+"""Terminal session management for tool instances."""
+
+import asyncio
+import os
+import pty
+import select
+import struct
+import fcntl
+import uuid
+from typing import Any
+
+
+class TerminalSession:
+    """Manages a single terminal session connected to a docker container."""
+
+    def __init__(self, session_id: str, instance_id: uuid.UUID, container_id: str) -> None:
+        self.session_id = session_id
+        self.instance_id = instance_id
+        self.container_id = container_id
+        self.process: asyncio.subprocess.Process | None = None
+        self._closed = False
+        self._master_fd: int | None = None
+        self._slave_fd: int | None = None
+
+    async def start(self) -> None:
+        """Start the docker exec process with a shell using a PTY."""
+        # Create a pseudo-terminal on the host
+        self._master_fd, self._slave_fd = pty.openpty()
+        
+        # Set the terminal size initially
+        self._set_terminal_size(80, 24)
+        
+        # Start docker exec with the slave fd as stdin/stdout/stderr
+        # Using -it because the slave fd IS a TTY
+        self.process = await asyncio.create_subprocess_exec(
+            "docker",
+            "exec",
+            "-it",
+            "-e",
+            "TERM=xterm",
+            self.container_id,
+            "bash",
+            "-il",
+            stdin=self._slave_fd,
+            stdout=self._slave_fd,
+            stderr=self._slave_fd,
+        )
+        
+        # Close slave fd in parent process
+        os.close(self._slave_fd)
+        self._slave_fd = None
+
+    def _set_terminal_size(self, cols: int, rows: int) -> None:
+        """Set the terminal size using TIOCSWINSZ."""
+        if self._master_fd is None:
+            return
+        # TIOCSWINSZ = 0x5414 on Linux
+        TIOCSWINSZ = 0x5414
+        size = struct.pack('HHHH', rows, cols, 0, 0)
+        try:
+            fcntl.ioctl(self._master_fd, TIOCSWINSZ, size)
+        except (OSError, IOError):
+            pass
+
+    async def read_output(self) -> bytes:
+        """Read output from the PTY master."""
+        if self._master_fd is None or self._closed:
+            return b""
+        try:
+            # Use select to check if data is available
+            readable, _, _ = select.select([self._master_fd], [], [], 0.1)
+            if readable:
+                return os.read(self._master_fd, 4096)
+            return b""
+        except (OSError, IOError, ValueError):
+            return b""
+
+    async def write_input(self, data: bytes) -> None:
+        """Write input to the PTY master."""
+        if self._master_fd is None or self._closed:
+            return
+        try:
+            os.write(self._master_fd, data)
+        except (OSError, IOError):
+            pass
+
+    async def resize(self, cols: int, rows: int) -> None:
+        """Resize the terminal."""
+        if self._closed:
+            return
+        self._set_terminal_size(cols, rows)
+
+    async def close(self) -> None:
+        """Close the session and cleanup."""
+        if self._closed:
+            return
+        self._closed = True
+
+        if self._master_fd is not None:
+            try:
+                os.close(self._master_fd)
+            except OSError:
+                pass
+            self._master_fd = None
+
+        if self.process is not None:
+            try:
+                self.process.kill()
+                await asyncio.wait_for(self.process.wait(), timeout=2.0)
+            except (asyncio.TimeoutError, ProcessLookupError):
+                pass
+
+    def is_alive(self) -> bool:
+        """Check if the session process is still running."""
+        if self.process is None:
+            return False
+        return self.process.returncode is None

apps/api/src/utils/git_control.py

@@ -0,0 +1,295 @@
+"""Git control utilities for repository operations."""
+
+import subprocess
+from dataclasses import dataclass, field
+from typing import Any
+
+
+def _run_git_command(repo_path: str, *args: str) -> str:
+    """Run a git command in the repository directory."""
+    result = subprocess.run(
+        ["git", *args],
+        cwd=repo_path,
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode != 0:
+        raise RuntimeError(f"Git command failed: {result.stderr}")
+    return result.stdout
+
+
+@dataclass
+class GitStatus:
+    """Represents the working directory status."""
+
+    branch: str
+    modified: list[str] = field(default_factory=list)
+    added: list[str] = field(default_factory=list)
+    deleted: list[str] = field(default_factory=list)
+    untracked: list[str] = field(default_factory=list)
+    renamed: list[str] = field(default_factory=list)
+    ahead: int = 0
+    behind: int = 0
+
+
+def get_status(repo_path: str) -> GitStatus:
+    """Get the working directory status.
+
+    Args:
+        repo_path: Path to the git repository
+
+    Returns:
+        GitStatus with changes
+    """
+    # Get current branch
+    try:
+        branch = _run_git_command(repo_path, "rev-parse", "--abbrev-ref", "HEAD").strip()
+    except RuntimeError:
+        try:
+            branch = _run_git_command(repo_path, "symbolic-ref", "--short", "HEAD").strip()
+        except RuntimeError:
+            branch = "HEAD"
+
+    status = GitStatus(branch=branch)
+
+    # Get status with porcelain format
+    try:
+        output = _run_git_command(repo_path, "status", "--porcelain", "--branch")
+    except RuntimeError:
+        return status
+
+    for line in output.strip().split("\n"):
+        if not line:
+            continue
+
+        # Branch info line starts with ##
+        if line.startswith("## "):
+            branch_info = line[3:]
+            # Parse ahead/behind info
+            if "[ahead " in branch_info:
+                ahead_str = branch_info.split("[ahead ")[1].split("]")[0]
+                status.ahead = int(ahead_str.split(",")[0])
+            if "[behind " in branch_info:
+                behind_str = branch_info.split("[behind ")[1].split("]")[0]
+                status.behind = int(behind_str.split(",")[0])
+            continue
+
+        # Parse status code
+        if len(line) < 3:
+            continue
+
+        index_status = line[0]
+        worktree_status = line[1]
+        filename = line[3:]
+
+        # Untracked files
+        if index_status == "?" and worktree_status == "?":
+            status.untracked.append(filename)
+            continue
+
+        # Added files
+        if index_status == "A" or worktree_status == "A":
+            status.added.append(filename)
+            continue
+
+        # Deleted files
+        if index_status == "D" or worktree_status == "D":
+            status.deleted.append(filename)
+            continue
+
+        # Renamed files
+        if index_status == "R" or worktree_status == "R":
+            status.renamed.append(filename)
+            continue
+
+        # Modified files
+        if index_status == "M" or worktree_status == "M":
+            status.modified.append(filename)
+            continue
+
+    return status
+
+
+def create_branch(repo_path: str, name: str, base_branch: str = "HEAD") -> None:
+    """Create a new branch.
+
+    Args:
+        repo_path: Path to the git repository
+        name: Branch name
+        base_branch: Base branch to create from (default: HEAD)
+
+    Raises:
+        RuntimeError: If branch creation fails
+    """
+    try:
+        _run_git_command(repo_path, "rev-parse", "--verify", "HEAD^{commit}")
+    except RuntimeError:
+        _run_git_command(repo_path, "checkout", "--orphan", name)
+        return
+
+    _run_git_command(repo_path, "branch", name, base_branch)
+
+
+def delete_branch(repo_path: str, name: str, force: bool = False) -> None:
+    """Delete a branch.
+
+    Args:
+        repo_path: Path to the git repository
+        name: Branch name
+        force: Force delete even if not merged
+
+    Raises:
+        RuntimeError: If branch deletion fails
+    """
+    flag = "-D" if force else "-d"
+    _run_git_command(repo_path, "branch", flag, name)
+
+
+def checkout_branch(repo_path: str, name: str) -> None:
+    """Checkout a branch.
+
+    Args:
+        repo_path: Path to the git repository
+        name: Branch name
+
+    Raises:
+        RuntimeError: If checkout fails
+    """
+    _run_git_command(repo_path, "checkout", name)
+
+
+def commit_changes(
+    repo_path: str,
+    message: str,
+    author_name: str,
+    author_email: str,
+    files: list[str] | None = None,
+) -> str:
+    """Commit changes to the repository.
+
+    Args:
+        repo_path: Path to the git repository
+        message: Commit message
+        author_name: Author name
+        author_email: Author email
+        files: Specific files to commit (None = all staged)
+
+    Returns:
+        Commit hash
+
+    Raises:
+        RuntimeError: If commit fails
+    """
+    # Stage files if specified
+    if files:
+        for file in files:
+            _run_git_command(repo_path, "add", file)
+    else:
+        _run_git_command(repo_path, "add", "-A")
+
+    # Commit
+    _run_git_command(
+        repo_path,
+        "commit",
+        "-m",
+        message,
+        f"--author={author_name} <{author_email}>",
+    )
+
+    # Return commit hash
+    return _run_git_command(repo_path, "rev-parse", "HEAD").strip()
+
+
+def fetch(repo_path: str) -> None:
+    """Fetch from remote.
+
+    Args:
+        repo_path: Path to the git repository
+
+    Raises:
+        RuntimeError: If fetch fails
+    """
+    _run_git_command(repo_path, "fetch", "--all")
+
+
+def pull(repo_path: str, branch: str | None = None) -> None:
+    """Pull updates from remote.
+
+    Args:
+        repo_path: Path to the git repository
+        branch: Branch to pull (default: current branch)
+
+    Raises:
+        RuntimeError: If pull fails
+    """
+    args = ["pull"]
+    if branch:
+        args.append("origin")
+        args.append(branch)
+    _run_git_command(repo_path, *args)
+
+
+def push(repo_path: str, branch: str | None = None) -> None:
+    """Push changes to remote.
+
+    Args:
+        repo_path: Path to the git repository
+        branch: Branch to push (default: current branch)
+
+    Raises:
+        RuntimeError: If push fails
+    """
+    args = ["push"]
+    if branch:
+        args.extend(["origin", branch])
+    _run_git_command(repo_path, *args)
+
+
+def merge(
+    repo_path: str,
+    source_branch: str,
+    target_branch: str | None = None,
+    message: str | None = None,
+) -> str:
+    """Merge a branch into the current branch.
+
+    Args:
+        repo_path: Path to the git repository
+        source_branch: Branch to merge from
+        target_branch: Branch to merge into (default: current branch)
+        message: Merge commit message
+
+    Returns:
+        Merge commit hash
+
+    Raises:
+        RuntimeError: If merge fails (including conflicts)
+    """
+    # Checkout target branch if specified
+    if target_branch:
+        checkout_branch(repo_path, target_branch)
+
+    # Merge
+    args = ["merge", source_branch]
+    if message:
+        args.extend(["-m", message])
+
+    _run_git_command(repo_path, *args)
+
+    # Return merge commit hash
+    return _run_git_command(repo_path, "rev-parse", "HEAD").strip()
+
+
+def get_current_branch(repo_path: str) -> str:
+    """Get the current branch name.
+
+    Args:
+        repo_path: Path to the git repository
+
+    Returns:
+        Current branch name
+    """
+    try:
+        return _run_git_command(repo_path, "rev-parse", "--abbrev-ref", "HEAD").strip()
+    except RuntimeError:
+        return _run_git_command(repo_path, "symbolic-ref", "--short", "HEAD").strip()

apps/api/src/utils/git_files.py

@@ -0,0 +1,439 @@
+"""Git file utilities for browsing repository contents."""
+
+import logging
+import subprocess
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+
+@dataclass
+class FileTreeEntry:
+    """Represents a file or directory in the repository."""
+
+    name: str
+    type: str  # "file" or "directory"
+    path: str
+    size: int | None = None
+    mode: str | None = None
+    last_commit: dict[str, Any] | None = None
+
+
+@dataclass
+class BranchInfo:
+    """Represents a git branch."""
+
+    name: str
+    is_default: bool
+    last_commit: dict[str, Any] | None = None
+
+
+@dataclass
+class FileContent:
+    """Represents file content and metadata."""
+
+    path: str
+    branch: str
+    content: str
+    size: int
+    encoding: str
+    language: str | None
+    is_binary: bool
+    last_commit: dict[str, Any] | None = None
+
+
+def _run_git_command(repo_path: str, *args: str) -> str:
+    """Run a git command in the repository directory."""
+    result = subprocess.run(
+        ["git", *args],
+        cwd=repo_path,
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode != 0:
+        stderr = result.stderr
+        # Handle "dubious ownership" security error
+        if "dubious ownership" in stderr.lower():
+            logger.warning("Git ownership mismatch for %s, adding to safe.directory", repo_path)
+            # Add this directory to git's safe.directory list
+            subprocess.run(
+                ["git", "config", "--global", "--add", "safe.directory", repo_path],
+                capture_output=True,
+            )
+            # Retry the command
+            result = subprocess.run(
+                ["git", *args],
+                cwd=repo_path,
+                capture_output=True,
+                text=True,
+            )
+            if result.returncode == 0:
+                return result.stdout
+            stderr = result.stderr
+        raise RuntimeError(f"Git command failed: {stderr}")
+    return result.stdout
+
+
+logger = logging.getLogger(__name__)
+
+def list_tree(repo_path: str, branch: str = "main", path: str = "") -> list[FileTreeEntry]:
+    """List files and directories in a repository path.
+
+    Args:
+        repo_path: Path to the git repository
+        branch: Branch name to list from
+        path: Directory path within the repository (empty for root)
+
+    Returns:
+        List of FileTreeEntry objects
+    """
+    tree_path = f"{branch}:{path}" if path else branch
+
+    try:
+        output = _run_git_command(repo_path, "ls-tree", "-l", tree_path)
+    except RuntimeError as e:
+        logger.warning("git ls-tree failed for %s with branch '%s': %s", repo_path, tree_path, str(e))
+        # Try with HEAD if branch doesn't exist
+        tree_path = f"HEAD:{path}" if path else "HEAD"
+        try:
+            output = _run_git_command(repo_path, "ls-tree", "-l", tree_path)
+        except RuntimeError as e:
+            logger.error("git ls-tree failed for %s with HEAD: %s", repo_path, str(e))
+            # Check if this is an empty repository (no commits yet)
+            error_msg = str(e).lower()
+            if "not a valid object name" in error_msg or "does not exist" in error_msg:
+                # Empty repository - return empty list
+                return []
+            raise
+
+    entries = []
+    for line in output.strip().split("\n"):
+        if not line:
+            continue
+
+        # Format: <mode> <type> <hash> <size>\t<name>
+        parts = line.split("\t", 1)
+        if len(parts) != 2:
+            continue
+
+        meta, name = parts
+        meta_parts = meta.split()
+        if len(meta_parts) < 4:
+            continue
+
+        mode = meta_parts[0]
+        obj_type = meta_parts[1]
+        _ = meta_parts[2]  # object hash, not used
+        size = int(meta_parts[3]) if obj_type == "blob" else None
+
+        entry_path = f"{path}/{name}" if path else name
+
+        # Get last commit info for this entry
+        last_commit = _get_last_commit_for_path(repo_path, branch, entry_path)
+
+        entries.append(
+            FileTreeEntry(
+                name=name,
+                type="directory" if obj_type == "tree" else "file",
+                path=entry_path,
+                size=size,
+                mode=mode,
+                last_commit=last_commit,
+            )
+        )
+
+    return entries
+
+
+def _get_last_commit_for_path(repo_path: str, branch: str, path: str) -> dict[str, Any] | None:
+    """Get the last commit that modified a path."""
+    try:
+        output = _run_git_command(
+            repo_path,
+            "log",
+            "-1",
+            "--format=%H|%s|%an|%aI",
+            branch,
+            "--",
+            path,
+        )
+        if not output.strip():
+            return None
+
+        parts = output.strip().split("|", 3)
+        if len(parts) != 4:
+            return None
+
+        return {
+            "hash": parts[0],
+            "message": parts[1],
+            "author": parts[2],
+            "date": parts[3],
+        }
+    except RuntimeError:
+        return None
+
+
+def get_file_content(repo_path: str, branch: str, path: str) -> FileContent:
+    """Get the content of a file.
+
+    Args:
+        repo_path: Path to the git repository
+        branch: Branch name
+        path: File path within the repository
+
+    Returns:
+        FileContent with content and metadata
+    """
+    # Check if file exists
+    try:
+        _run_git_command(repo_path, "cat-file", "-e", f"{branch}:{path}")
+    except RuntimeError:
+        raise FileNotFoundError(f"File '{path}' not found in branch '{branch}'")
+
+    # Get file size
+    size_output = _run_git_command(repo_path, "cat-file", "-s", f"{branch}:{path}")
+    size = int(size_output.strip())
+
+    # Check if binary
+    is_binary = _is_binary_file(repo_path, branch, path)
+
+    # Get content (only for text files)
+    content = ""
+    if not is_binary:
+        content = _run_git_command(repo_path, "show", f"{branch}:{path}")
+
+    # Detect language from extension
+    language = _detect_language(path)
+
+    # Get last commit
+    last_commit = _get_last_commit_for_path(repo_path, branch, path)
+
+    return FileContent(
+        path=path,
+        branch=branch,
+        content=content,
+        size=size,
+        encoding="utf-8",
+        language=language,
+        is_binary=is_binary,
+        last_commit=last_commit,
+    )
+
+
+def _is_binary_file(repo_path: str, branch: str, path: str) -> bool:
+    """Check if a file is binary using raw bytes to avoid encoding issues."""
+    try:
+        result = subprocess.run(
+            ["git", "show", f"{branch}:{path}"],
+            cwd=repo_path,
+            capture_output=True,
+        )
+        if result.returncode != 0:
+            raise RuntimeError(f"Git command failed: {result.stderr.decode()}")
+        # A file is binary if it contains null bytes
+        return b"\x00" in result.stdout
+    except RuntimeError:
+        return True
+
+
+def _detect_language(path: str) -> str | None:
+    """Detect programming language from file extension."""
+    ext = Path(path).suffix.lower()
+    language_map = {
+        ".py": "python",
+        ".js": "javascript",
+        ".ts": "typescript",
+        ".jsx": "jsx",
+        ".tsx": "tsx",
+        ".html": "html",
+        ".css": "css",
+        ".scss": "scss",
+        ".json": "json",
+        ".md": "markdown",
+        ".yaml": "yaml",
+        ".yml": "yaml",
+        ".sh": "bash",
+        ".rs": "rust",
+        ".go": "go",
+        ".java": "java",
+        ".c": "c",
+        ".cpp": "cpp",
+        ".h": "c",
+        ".php": "php",
+        ".rb": "ruby",
+        ".sql": "sql",
+        ".dockerfile": "dockerfile",
+        ".vue": "vue",
+        ".svelte": "svelte",
+    }
+    return language_map.get(ext)
+
+
+def list_branches(repo_path: str) -> tuple[list[BranchInfo], str]:
+    """List all branches and identify the default branch.
+
+    Args:
+        repo_path: Path to the git repository
+
+    Returns:
+        Tuple of (list of BranchInfo, default branch name)
+    """
+    # Get all branches
+    try:
+        output = _run_git_command(repo_path, "branch", "-a", "--format=%(refname:short)")
+    except RuntimeError as e:
+        logger.error("Failed to list branches for %s: %s", repo_path, str(e))
+        raise
+
+    branches: list[BranchInfo] = []
+    default_branch = "main"
+
+    for line in output.strip().split("\n"):
+        if not line:
+            continue
+
+        branch_name = line.strip()
+        # Skip remote tracking branches (they start with remotes/)
+        if branch_name.startswith("remotes/"):
+            # Extract just the branch name part
+            parts = branch_name.split("/", 2)
+            if len(parts) >= 3:
+                branch_name = parts[2]
+            else:
+                continue
+
+        # Skip duplicates
+        if any(b.name == branch_name for b in branches):
+            continue
+
+        # Check if this is the default branch (HEAD points to it)
+        try:
+            head_output = _run_git_command(
+                repo_path,
+                "symbolic-ref",
+                "HEAD",
+            )
+            if head_output.strip() == f"refs/heads/{branch_name}":
+                default_branch = branch_name
+        except RuntimeError:
+            pass
+
+        # Get last commit for branch
+        last_commit = _get_last_commit_for_path(repo_path, branch_name, ".")
+
+        branches.append(
+            BranchInfo(
+                name=branch_name,
+                is_default=(branch_name == default_branch),
+                last_commit=last_commit,
+            )
+        )
+
+    # If no branches found, try to get HEAD
+    if not branches:
+        try:
+            output = _run_git_command(repo_path, "rev-parse", "--abbrev-ref", "HEAD")
+            branch_name = output.strip()
+            if branch_name and branch_name != "HEAD":
+                last_commit = _get_last_commit_for_path(repo_path, branch_name, ".")
+                branches.append(
+                    BranchInfo(
+                        name=branch_name,
+                        is_default=True,
+                        last_commit=last_commit,
+                    )
+                )
+                default_branch = branch_name
+        except RuntimeError:
+            try:
+                output = _run_git_command(repo_path, "symbolic-ref", "--short", "HEAD")
+                branch_name = output.strip()
+                if branch_name:
+                    branches.append(
+                        BranchInfo(
+                            name=branch_name,
+                            is_default=True,
+                            last_commit=None,
+                        )
+                    )
+                    default_branch = branch_name
+            except RuntimeError:
+                pass
+
+    return branches, default_branch
+
+
+def commit_file(
+    repo_path: str,
+    branch: str,
+    path: str,
+    content: str,
+    commit_message: str,
+    author_name: str,
+    author_email: str,
+) -> str:
+    """Commit a file change.
+
+    Args:
+        repo_path: Path to the git repository
+        branch: Branch to commit to
+        path: File path within the repository
+        content: New file content
+        commit_message: Commit message
+        author_name: Author name
+        author_email: Author email
+
+    Returns:
+        Commit hash
+    """
+    # For bare repositories, we need to use git commands differently
+    # We'll create a temporary worktree, make changes, and commit
+
+    import tempfile
+    import os
+
+    # Create a temporary worktree
+    with tempfile.TemporaryDirectory() as worktree_path:
+        # Add worktree
+        _run_git_command(
+            repo_path,
+            "worktree",
+            "add",
+            "--detach",
+            worktree_path,
+            branch,
+        )
+
+        try:
+            # Write file content
+            file_path = os.path.join(worktree_path, path)
+            os.makedirs(os.path.dirname(file_path), exist_ok=True)
+            with open(file_path, "w", encoding="utf-8") as f:
+                f.write(content)
+
+            # Configure git author
+            _run_git_command(worktree_path, "config", "user.name", author_name)
+            _run_git_command(worktree_path, "config", "user.email", author_email)
+
+            # Stage and commit
+            _run_git_command(worktree_path, "add", path)
+            _run_git_command(
+                worktree_path,
+                "commit",
+                "-m",
+                commit_message,
+            )
+
+            # Get commit hash
+            commit_hash = _run_git_command(
+                worktree_path,
+                "rev-parse",
+                "HEAD",
+            ).strip()
+
+            return commit_hash
+
+        finally:
+            # Remove worktree
+            _run_git_command(repo_path, "worktree", "remove", worktree_path)

apps/api/src/utils/git_history.py

@@ -0,0 +1,382 @@
+"""Git history extraction utilities for bare/mirror repositories."""
+
+import subprocess
+from dataclasses import dataclass
+from datetime import datetime, timezone
+from typing import Any
+
+
+@dataclass
+class Commit:
+    """Represents a single git commit."""
+
+    hash: str
+    short_hash: str
+    parents: list[str]
+    author: str
+    email: str
+    date: str
+    timestamp: int
+    message: str
+    branches: list[str]
+    tags: list[str]
+
+
+@dataclass
+class FileChange:
+    """Represents a changed file in a commit."""
+
+    path: str
+    change_type: str
+    insertions: int
+    deletions: int
+    diff: str
+
+
+@dataclass
+class CommitDetail(Commit):
+    """Extended commit info with diff."""
+
+    body: str
+    stats: dict[str, int]
+    files: list[FileChange]
+
+
+def _run_git_command(repo_path: str, args: list[str]) -> str:
+    """Execute a git command in the repository directory."""
+    result = subprocess.run(
+        ["git", "-C", repo_path, *args],
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+    if result.returncode != 0:
+        raise RuntimeError(f"Git command failed: {result.stderr}")
+    return result.stdout
+
+
+def get_commit_history(repo_path: str, branch: str | None = None, limit: int = 100, offset: int = 0) -> dict[str, Any]:
+    """Extract commit history from a git repository.
+
+    Returns structured data including commits, branches, and graph information.
+    """
+    # Get list of branches
+    branches_output = _run_git_command(repo_path, ["branch", "-a", "--format=%(refname:short)"])
+    branches = [b.strip() for b in branches_output.strip().split("\n") if b.strip()]
+
+    # Build git log command - use NULL bytes as separators to avoid parsing issues
+    log_args = [
+        "log",
+        "--format=%H%x00%P%x00%an%x00%ae%x00%at%x00%s",
+        f"--max-count={limit}",
+        f"--skip={offset}",
+    ]
+    if branch:
+        log_args.append(branch)
+    else:
+        log_args.append("--all")
+
+    log_output = _run_git_command(repo_path, log_args)
+
+    # Get branch info for each commit
+    branch_map = _get_branch_map(repo_path)
+    tag_map = _get_tag_map(repo_path)
+
+    commits = []
+    log_lines = log_output.strip().split("\n") if log_output.strip() else []
+
+    for line in log_lines:
+        line = line.strip()
+        if not line:
+            continue
+
+        parts = line.split("\x00")
+        if len(parts) < 6:
+            continue
+
+        commit_hash = parts[0]
+        parents = parts[1].split() if parts[1] else []
+
+        commits.append(
+            Commit(
+                hash=commit_hash,
+                short_hash=commit_hash[:7],
+                parents=parents,
+                author=parts[2],
+                email=parts[3],
+                date=parts[4],
+                timestamp=int(parts[4]),
+                message=parts[5],
+                branches=branch_map.get(commit_hash, []),
+                tags=tag_map.get(commit_hash, []),
+            )
+        )
+
+    # Get total commit count
+    count_output = _run_git_command(repo_path, ["rev-list", "--all", "--count"])
+    total_commits = int(count_output.strip()) if count_output.strip() else 0
+
+    # Build graph data and generate graph symbols
+    graph_data = _build_graph_data(commits)
+    
+    # Generate simple graph symbols based on parent count
+    commit_dicts = []
+    for i, commit in enumerate(commits):
+        if len(commit.parents) == 0:
+            graph_symbol = "○"  # Initial commit
+        elif len(commit.parents) > 1:
+            graph_symbol = "●"  # Merge commit
+        else:
+            graph_symbol = "○"  # Regular commit
+        
+        # Simple depth calculation based on merge status
+        graph_depth = min(len(commit.parents), 3)
+        
+        commit_dicts.append(_commit_to_dict(commit, graph_symbol, graph_depth))
+
+    return {
+        "commits": commit_dicts,
+        "branches": branches,
+        "total_commits": total_commits,
+        "graph_data": graph_data,
+    }
+
+
+def get_commit_detail(repo_path: str, commit_hash: str) -> dict[str, Any]:
+    """Get detailed information about a specific commit."""
+    # Get commit metadata
+    format_str = "%H|%P|%an|%ae|%at|%s|%b"
+    log_output = _run_git_command(
+        repo_path, ["log", "-1", f"--format={format_str}", commit_hash]
+    )
+
+    parts = log_output.strip().split("|", 6)
+    if len(parts) < 6:
+        raise ValueError(f"Invalid commit: {commit_hash}")
+
+    commit_hash = parts[0]
+    parents = parts[1].split() if parts[1] else []
+    author = parts[2]
+    email = parts[3]
+    timestamp = int(parts[4])
+    message = parts[5]
+    body = parts[6] if len(parts) > 6 else ""
+
+    # Get stats
+    stat_output = _run_git_command(
+        repo_path, ["show", "--stat", "--format=", commit_hash]
+    )
+    stats = _parse_stats(stat_output)
+
+    # Get diff
+    diff_output = _run_git_command(
+        repo_path, ["show", "--format=", commit_hash]
+    )
+    files = _parse_diff(diff_output)
+
+    # Get branch/tag info
+    branch_map = _get_branch_map(repo_path)
+    tag_map = _get_tag_map(repo_path)
+
+    return {
+        "hash": commit_hash,
+        "short_hash": commit_hash[:7],
+        "parents": parents,
+        "author_name": author,
+        "author_email": email,
+        "author_date": datetime.fromtimestamp(timestamp, tz=timezone.utc).isoformat(),
+        "committer_name": author,  # TODO: extract committer separately
+        "committer_email": email,  # TODO: extract committer separately
+        "committer_date": datetime.fromtimestamp(timestamp, tz=timezone.utc).isoformat(),
+        "message": message,
+        "body": body,
+        "branches": branch_map.get(commit_hash, []),
+        "tags": tag_map.get(commit_hash, []),
+        "stats": stats,
+        "diff": diff_output,
+        "files": [_file_change_to_dict(f) for f in files],
+    }
+
+
+def _get_branch_map(repo_path: str) -> dict[str, list[str]]:
+    """Build a mapping of commit hash to branch names."""
+    result = {}
+    branch_output = _run_git_command(
+        repo_path, ["for-each-ref", "--format=%(objectname) %(refname:short)", "refs/heads/"]
+    )
+
+    for line in branch_output.strip().split("\n"):
+        if " " in line:
+            commit_hash, branch_name = line.split(" ", 1)
+            if commit_hash not in result:
+                result[commit_hash] = []
+            result[commit_hash].append(branch_name)
+
+    return result
+
+
+def _get_tag_map(repo_path: str) -> dict[str, list[str]]:
+    """Build a mapping of commit hash to tag names."""
+    result = {}
+    tag_output = _run_git_command(
+        repo_path, ["for-each-ref", "--format=%(objectname) %(refname:short)", "refs/tags/"]
+    )
+
+    for line in tag_output.strip().split("\n"):
+        if " " in line:
+            commit_hash, tag_name = line.split(" ", 1)
+            if commit_hash not in result:
+                result[commit_hash] = []
+            result[commit_hash].append(tag_name)
+
+    return result
+
+
+def _build_graph_data(commits: list[Commit]) -> dict[str, Any]:
+    """Build graph visualization data from commits."""
+    if not commits:
+        return {"nodes": [], "edges": []}
+
+    # Create hash to index mapping
+    hash_to_idx = {c.hash: i for i, c in enumerate(commits)}
+
+    nodes = []
+    edges = []
+
+    for i, commit in enumerate(commits):
+        # Calculate column based on branch
+        column = 0
+        if commit.branches:
+            # Use first branch as column indicator
+            column = hash(commit.branches[0]) % 5
+
+        nodes.append(
+            {
+                "hash": commit.hash,
+                "x": column * 60 + 30,
+                "y": i * 50 + 25,
+                "column": column,
+            }
+        )
+
+        # Create edges to parents
+        for parent_hash in commit.parents:
+            if parent_hash in hash_to_idx:
+                edges.append(
+                    {
+                        "from_hash": commit.hash,
+                        "to_hash": parent_hash,
+                        "type": "parent",
+                    }
+                )
+
+    return {"nodes": nodes, "edges": edges}
+
+
+def _parse_stats(stat_output: str) -> dict[str, int]:
+    """Parse git show --stat output."""
+    lines = stat_output.strip().split("\n")
+    stats = {"files_changed": 0, "insertions": 0, "deletions": 0}
+
+    for line in lines:
+        line = line.strip()
+        if "files changed" in line or "file changed" in line:
+            # Parse summary line like "3 files changed, 45 insertions(+), 12 deletions(-)"
+            parts = line.split(",")
+            for part in parts:
+                part = part.strip()
+                if "file" in part:
+                    try:
+                        stats["files_changed"] = int(part.split()[0])
+                    except (ValueError, IndexError):
+                        pass
+                elif "insertion" in part:
+                    try:
+                        stats["insertions"] = int(part.split()[0])
+                    except (ValueError, IndexError):
+                        pass
+                elif "deletion" in part:
+                    try:
+                        stats["deletions"] = int(part.split()[0])
+                    except (ValueError, IndexError):
+                        pass
+
+    return stats
+
+
+def _parse_diff(diff_output: str) -> list[FileChange]:
+    """Parse git diff output into file changes."""
+    files = []
+    current_file = None
+    current_diff = []
+
+    for line in diff_output.split("\n"):
+        if line.startswith("diff --git"):
+            # Save previous file
+            if current_file:
+                current_file.diff = "\n".join(current_diff)
+                files.append(current_file)
+
+            # Start new file
+            current_diff = [line]
+            current_file = FileChange(
+                path="",
+                change_type="modified",
+                insertions=0,
+                deletions=0,
+                diff="",
+            )
+        elif line.startswith("--- ") or line.startswith("+++ "):
+            current_diff.append(line)
+            if line.startswith("+++ ") and not line.startswith("+++ /dev/null"):
+                current_file.path = line[6:]
+        elif line.startswith("@@ "):
+            current_diff.append(line)
+        elif line.startswith("+") and not line.startswith("+++"):
+            current_diff.append(line)
+            current_file.insertions += 1
+        elif line.startswith("-") and not line.startswith("---"):
+            current_diff.append(line)
+            current_file.deletions += 1
+        elif current_file:
+            current_diff.append(line)
+
+    # Save last file
+    if current_file:
+        current_file.diff = "\n".join(current_diff)
+        files.append(current_file)
+
+    return files
+
+
+def _commit_to_dict(commit: Commit, graph_symbol: str = "", graph_depth: int = 0) -> dict[str, Any]:
+    """Convert Commit dataclass to dictionary."""
+    refs = []
+    if commit.branches:
+        refs.extend(commit.branches)
+    if commit.tags:
+        refs.extend(commit.tags)
+    
+    return {
+        "hash": commit.hash,
+        "short_hash": commit.short_hash,
+        "parents": commit.parents,
+        "author_name": commit.author,
+        "author_email": commit.email,
+        "author_date": datetime.fromtimestamp(commit.timestamp, tz=timezone.utc).isoformat(),
+        "message": commit.message,
+        "refs": refs,
+        "graph_symbol": graph_symbol,
+        "graph_depth": graph_depth,
+    }
+
+
+def _file_change_to_dict(file_change: FileChange) -> dict[str, Any]:
+    """Convert FileChange dataclass to dictionary."""
+    return {
+        "path": file_change.path,
+        "change_type": file_change.change_type,
+        "insertions": file_change.insertions,
+        "deletions": file_change.deletions,
+        "diff": file_change.diff,
+    }

apps/api/src/utils/git_url_parser.py

@@ -0,0 +1,228 @@
+"""Git URL parsing utilities to extract base repository URLs from browser URLs."""
+
+from urllib.parse import urlparse
+
+
+def extract_base_repo_url(url: str) -> str | None:
+    """Extract base repository URL from a browser/git URL.
+
+    Examples:
+        https://github.com/user/repo/tree/main → https://github.com/user/repo.git
+        https://github.com/user/repo.git → https://github.com/user/repo.git
+        git@github.com:user/repo.git → git@github.com:user/repo.git
+        https://gitlab.com/user/repo/-/blob/main/README.md → https://gitlab.com/user/repo.git
+
+    Returns None if URL doesn't match known patterns.
+    """
+    # Handle SSH URLs (pass through unchanged)
+    if url.startswith("git@"):
+        return url if url.endswith(".git") else f"{url}.git"
+
+    try:
+        parsed = urlparse(url)
+    except Exception:
+        return None
+
+    # Remove query parameters
+    url = f"{parsed.scheme}://{parsed.netloc}{parsed.path}"
+
+    # Extract host
+    host = parsed.netloc.lower()
+
+    # Split path
+    path_parts = [p for p in parsed.path.split("/") if p]
+
+    if not path_parts:
+        return None
+
+    # Determine host type and extract base
+    if "github.com" in host:
+        return _extract_github_url(url, path_parts)
+    elif "gitlab.com" in host:
+        return _extract_gitlab_url(url, path_parts)
+    elif "bitbucket.org" in host:
+        return _extract_bitbucket_url(url, path_parts)
+    else:
+        # Generic host - try basic extraction
+        return _extract_generic_url(url, path_parts)
+
+
+def _extract_github_url(url: str, path_parts: list[str]) -> str | None:
+    """Extract base repo URL from GitHub URL."""
+    # Need at least owner/repo
+    if len(path_parts) < 2:
+        return None
+
+    # Find the repo name (second path part)
+    # Remove trailing .git if present
+    repo_name = path_parts[1]
+    if repo_name.endswith(".git"):
+        repo_name = repo_name[:-4]
+
+    # Reconstruct base URL
+    base = f"https://github.com/{path_parts[0]}/{repo_name}"
+
+    # Add .git suffix
+    return f"{base}.git"
+
+
+def _extract_gitlab_url(url: str, path_parts: list[str]) -> str | None:
+    """Extract base repo URL from GitLab URL."""
+    # Need at least owner/repo
+    if len(path_parts) < 2:
+        return None
+
+    # Find the repo name (second path part)
+    repo_name = path_parts[1]
+    if repo_name.endswith(".git"):
+        repo_name = repo_name[:-4]
+
+    # Reconstruct base URL
+    base = f"https://gitlab.com/{path_parts[0]}/{repo_name}"
+
+    return f"{base}.git"
+
+
+def _extract_bitbucket_url(url: str, path_parts: list[str]) -> str | None:
+    """Extract base repo URL from Bitbucket URL."""
+    # Need at least owner/repo
+    if len(path_parts) < 2:
+        return None
+
+    # Find the repo name (second path part)
+    repo_name = path_parts[1]
+    if repo_name.endswith(".git"):
+        repo_name = repo_name[:-4]
+
+    # Reconstruct base URL
+    base = f"https://bitbucket.org/{path_parts[0]}/{repo_name}"
+
+    return f"{base}.git"
+
+
+def _extract_generic_url(url: str, path_parts: list[str]) -> str | None:
+    """Extract base repo URL from generic git host URL."""
+    # Need at least owner/repo
+    if len(path_parts) < 2:
+        return None
+
+    # Find the repo name (second path part)
+    repo_name = path_parts[1]
+    if repo_name.endswith(".git"):
+        repo_name = repo_name[:-4]
+
+    # Reconstruct base URL
+    parsed = urlparse(url)
+    base = f"{parsed.scheme}://{parsed.netloc}/{path_parts[0]}/{repo_name}"
+
+    return f"{base}.git"
+
+
+def is_valid_clone_url(url: str) -> bool:
+    """Check if URL is already a valid git clone URL.
+
+    A valid clone URL:
+    - Is an SSH URL (git@host:path)
+    - Ends with .git
+    - Has no browser-specific path segments
+    """
+    # SSH URLs are always valid
+    if url.startswith("git@"):
+        return True
+
+    try:
+        parsed = urlparse(url)
+    except Exception:
+        return False
+
+    path = parsed.path
+
+    # Must end with .git for HTTPS
+    if not path.endswith(".git"):
+        return False
+
+    # Check for browser-specific paths
+    browser_paths = ["/tree/", "/blob/", "/pull/", "/issues/", "/actions/",
+                     "-/tree/", "-/blob/", "-/merge_requests/",
+                     "/src/"]
+
+    for bp in browser_paths:
+        if bp in path:
+            return False
+
+    return True
+
+
+def parse_git_url(url: str) -> dict:
+    """Parse a git URL and return detailed information.
+
+    Returns:
+        {
+            "original_url": str,
+            "base_url": str | None,
+            "is_valid_clone_url": bool,
+            "needs_parsing": bool,
+            "host": str | None,
+            "message": str,
+            "error_code": str | None,
+        }
+    """
+    result = {
+        "original_url": url,
+        "base_url": None,
+        "is_valid_clone_url": False,
+        "needs_parsing": False,
+        "host": None,
+        "message": "",
+        "error_code": None,
+    }
+
+    # Check if empty
+    if not url or not url.strip():
+        result["message"] = "Please enter a URL"
+        result["error_code"] = "INVALID_URL"
+        return result
+
+    url = url.strip()
+
+    # Try to parse
+    try:
+        parsed = urlparse(url)
+    except Exception:
+        result["message"] = "Please enter a valid URL"
+        result["error_code"] = "INVALID_URL"
+        return result
+
+    # Extract host
+    if parsed.netloc:
+        result["host"] = parsed.netloc.lower()
+    elif url.startswith("git@"):
+        # SSH URL: git@host:path
+        parts = url.split(":", 1)
+        if len(parts) == 2:
+            result["host"] = parts[0].replace("git@", "")
+    else:
+        result["message"] = "Please enter a valid URL"
+        result["error_code"] = "INVALID_URL"
+        return result
+
+    # Check if already valid
+    if is_valid_clone_url(url):
+        result["base_url"] = url
+        result["is_valid_clone_url"] = True
+        result["needs_parsing"] = False
+        result["message"] = "Valid git repository URL"
+        return result
+
+    # Try to extract base URL
+    base = extract_base_repo_url(url)
+    if base:
+        result["base_url"] = base
+        result["needs_parsing"] = True
+        result["message"] = f"This looks like a browser URL. Did you mean: {base}?"
+        result["error_code"] = "URL_NEEDS_PARSING"
+    else:
+        result["message"] = "Could not parse this URL. Please enter a valid git repository URL."
+        result["error_code"] = "INVALID_URL"
+
+    return result

apps/api/tests/conftest.py

@@ -3,6 +3,7 @@
 import asyncio
 import os
 from typing import AsyncGenerator, Generator
+from unittest.mock import patch
 
 import pytest
 import pytest_asyncio
@@ -11,82 +12,142 @@ from sqlalchemy import create_engine, text
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
 from sqlalchemy.orm import sessionmaker
 
+# Set test environment BEFORE importing app modules
+os.environ["APP_ENV"] = "testing"
+os.environ["SECRET_KEY"] = "test-secret-key-for-testing-only-do-not-use-in-production"
+os.environ["DATABASE_URL"] = "sqlite+aiosqlite:///:memory:"
+
 from src.config import Settings, build_database_url
 from src.models.base import Base
 from src.main import app
-
-
-# Unit test fixtures (SQLite in-memory)
-
-@pytest.fixture(scope="session")
-def sqlite_engine():
-    """Create a SQLite in-memory engine for unit tests."""
-    engine = create_engine("sqlite:///:memory:", connect_args={"check_same_thread": False})
-    Base.metadata.create_all(engine)
-    yield engine
-    engine.dispose()
-
-
-@pytest.fixture
-def sqlite_session(sqlite_engine) -> Generator:
-    """Provide a SQLite session for unit tests."""
-    connection = sqlite_engine.connect()
-    transaction = connection.begin()
-    session = sessionmaker(bind=connection)()
-    
-    yield session
-    
-    session.close()
-    transaction.rollback()
-    connection.close()
-
-
-# Integration test fixtures (PostgreSQL)
-
-TEST_DATABASE_URL = build_database_url(
-    user="headquarter",
-    password="headquarter",
-    host="localhost",
-    port=5432,
-    database="headquarter",
-)
-
-
-@pytest_asyncio.fixture(scope="session")
-async def postgres_engine():
-    """Create a PostgreSQL engine for integration tests."""
-    engine = create_async_engine(TEST_DATABASE_URL)
-    async with engine.begin() as conn:
-        await conn.run_sync(Base.metadata.create_all)
-    yield engine
-    await engine.dispose()
-
-
-@pytest_asyncio.fixture
-async def db_session(postgres_engine) -> AsyncGenerator[AsyncSession, None]:
-    """Provide a database session with transaction rollback."""
-    async with postgres_engine.connect() as connection:
-        transaction = await connection.begin_nested()
-        session_factory = async_sessionmaker(
-            connection, expire_on_commit=False, class_=AsyncSession
-        )
-        session = session_factory()
-        
-        yield session
-        
-        await session.close()
-        await transaction.rollback()
+from src.auth.dependencies import get_db_session
 
 
 @pytest.fixture
 def test_client() -> Generator[TestClient, None, None]:
-    """Provide a FastAPI test client."""
-    with TestClient(app) as client:
-        yield client
+    """Provide a FastAPI test client with SQLite database."""
+    # Create a single engine for this test
+    engine = create_async_engine(
+        "sqlite+aiosqlite:///:memory:",
+        connect_args={"check_same_thread": False},
+    )
+    
+    # Create tables
+    async def init_db():
+        async with engine.begin() as conn:
+            await conn.run_sync(Base.metadata.create_all)
+    
+    asyncio.run(init_db())
+    
+    async def override_get_db_session() -> AsyncGenerator[AsyncSession, None]:
+        async with async_sessionmaker(engine, expire_on_commit=False)() as session:
+            yield session
+
+    # Override the dependency
+    app.dependency_overrides[get_db_session] = override_get_db_session
+    
+    # Patch startup events to prevent PostgreSQL connection attempts
+    with patch("src.main.init_database") as mock_init, \
+         patch("src.main.seed_builtin_tool_types") as mock_seed:
+        mock_init.return_value = True
+        mock_seed.return_value = None
+        
+        try:
+            with TestClient(app) as client:
+                yield client
+        finally:
+            # Clean up overrides
+            app.dependency_overrides.pop(get_db_session, None)
+            asyncio.run(engine.dispose())
 
 
-@pytest.fixture(autouse=True)
-def configure_test_env(monkeypatch):
-    """Configure environment for testing."""
-    monkeypatch.setenv("DATABASE_URL", TEST_DATABASE_URL)
-    monkeypatch.setenv("APP_ENV", "testing")
+@pytest.fixture
+def authenticated_client(test_client) -> Generator[TestClient, None, None]:
+    """Provide an authenticated test client with a test user."""
+    import uuid
+    from src.auth.session import create_session_cookie
+    from src.models.user import User
+    
+    user_id = str(uuid.uuid4())
+    settings = Settings()
+    
+    # Create user in database using the same engine as test_client
+    # We need to access the engine from the test_client fixture
+    # Since we can't easily do that, we'll create the user via API call
+    # But we need the user to exist before any API calls
+    # So we need to create the user using the overridden dependency
+    
+    async def create_test_user():
+        # Get the override function
+        override_fn = app.dependency_overrides.get(get_db_session)
+        if override_fn:
+            gen = override_fn()
+            session = await gen.asend(None)
+            try:
+                user = User(
+                    id=uuid.UUID(user_id),
+                    email="test@headquarter.local",
+                    name="Test User",
+                    authentik_id=f"authentik-{user_id}",
+                    avatar_url=None,
+                )
+                session.add(user)
+                await session.commit()
+            finally:
+                await gen.aclose()
+    
+    asyncio.run(create_test_user())
+    
+    # Create session cookie
+    session_cookie = create_session_cookie(
+        settings=settings,
+        user_id=user_id,
+    )
+    
+    # Set cookie on client
+    test_client.cookies.set("session", session_cookie)
+    
+    yield test_client
+
+
+@pytest.fixture
+def admin_client(test_client) -> Generator[TestClient, None, None]:
+    """Provide an authenticated test client with an admin user."""
+    import uuid
+    from src.auth.session import create_session_cookie
+    from src.models.user import User
+    
+    user_id = str(uuid.uuid4())
+    settings = Settings()
+    
+    async def create_admin_user():
+        override_fn = app.dependency_overrides.get(get_db_session)
+        if override_fn:
+            gen = override_fn()
+            session = await gen.asend(None)
+            try:
+                user = User(
+                    id=uuid.UUID(user_id),
+                    email="admin@headquarter.local",
+                    name="Admin User",
+                    authentik_id=f"authentik-admin-{user_id}",
+                    avatar_url=None,
+                    is_admin=True,
+                )
+                session.add(user)
+                await session.commit()
+            finally:
+                await gen.aclose()
+    
+    asyncio.run(create_admin_user())
+    
+    # Create session cookie
+    session_cookie = create_session_cookie(
+        settings=settings,
+        user_id=user_id,
+    )
+    
+    # Set cookie on client
+    test_client.cookies.set("session", session_cookie)
+    
+    yield test_client

apps/api/tests/integration/test_auth_api.py

@@ -1,5 +1,4 @@
 import uuid
-from datetime import UTC, datetime, timedelta
 import asyncio
 import importlib
 
@@ -8,7 +7,7 @@ import pytest
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import create_async_engine
 
-from src.auth.jwt_service import mint_access_token
+from src.auth.session import create_session_cookie
 from src.config import Settings, build_database_url
 from src.models import Base
 from src.models.user import User
@@ -27,7 +26,7 @@ def _prepare_auth_test_db() -> None:
         )
         async with engine.begin() as connection:
             await connection.run_sync(Base.metadata.create_all)
-            await connection.execute(text("TRUNCATE TABLE refresh_tokens, users RESTART IDENTITY CASCADE"))
+            await connection.execute(text("TRUNCATE TABLE users RESTART IDENTITY CASCADE"))
         await engine.dispose()
 
     asyncio.run(_run())
@@ -44,7 +43,7 @@ def _load_app():
     return main_module.app
 
 
-def _insert_user_for_refresh(user_id: str) -> None:
+def _insert_test_user(user_id: str) -> None:
     async def _run() -> None:
         engine = create_async_engine(
             build_database_url(
@@ -63,9 +62,9 @@ def _insert_user_for_refresh(user_id: str) -> None:
         async with session_factory() as session:
             user = User(
                 id=uuid.UUID(user_id),
-                email="refresh@headquarter.local",
-                name="Refresh User",
-                authentik_id="refresh-user",
+                email="test@headquarter.local",
+                name="Test User",
+                authentik_id="test-user",
                 avatar_url=None,
             )
             await session.merge(user)
@@ -88,7 +87,7 @@ def test_login_redirects_to_authentik_authorize_endpoint() -> None:
 
 
 @pytest.mark.integration
-def test_me_returns_401_without_access_cookie() -> None:
+def test_me_returns_401_without_session_cookie() -> None:
     _prepare_auth_test_db()
     app = _load_app()
 
@@ -99,116 +98,33 @@ def test_me_returns_401_without_access_cookie() -> None:
 
 
 @pytest.mark.integration
-def test_me_returns_user_payload_with_valid_access_cookie() -> None:
+def test_me_returns_user_with_valid_session() -> None:
+    user_id = "11111111-1111-1111-1111-111111111111"
     _prepare_auth_test_db()
+    _insert_test_user(user_id)
     app = _load_app()
 
     settings = Settings()
-    token = mint_access_token(
-        settings=settings,
-        subject=str(uuid.uuid4()),
-        email="dev@headquarter.local",
-        name="Dev User",
-        expires_at=datetime.now(UTC) + timedelta(minutes=15),
-    )
+    session_cookie = create_session_cookie(settings=settings, user_id=user_id)
 
     client = TestClient(app)
-    client.cookies.set("access_token", token)
-    response = client.get("/auth/me")
+    response = client.get("/auth/me", cookies={"session": session_cookie})
 
     assert response.status_code == 200
-    assert response.json()["email"] == "dev@headquarter.local"
+    data = response.json()
+    assert data["email"] == "test@headquarter.local"
+    assert data["name"] == "Test User"
 
 
 @pytest.mark.integration
-def test_logout_clears_auth_cookies() -> None:
+def test_logout_clears_session_cookie() -> None:
     _prepare_auth_test_db()
     app = _load_app()
 
     client = TestClient(app)
-    client.cookies.set("refresh_token", "opaque-token")
     response = client.post("/auth/logout")
 
     assert response.status_code == 200
-    assert "access_token=" in response.headers.get("set-cookie", "")
-
-
-@pytest.mark.integration
-def test_callback_rejects_mismatched_state() -> None:
-    _prepare_auth_test_db()
-    app = _load_app()
-
-    client = TestClient(app)
-    client.cookies.set("auth_state", "expected")
-    response = client.get("/auth/callback?code=test-code&state=wrong")
-
-    assert response.status_code == 401
-
-
-@pytest.mark.integration
-def test_callback_sets_auth_cookies_after_success(monkeypatch) -> None:
-    _prepare_auth_test_db()
-    app = _load_app()
-
-    async def fake_exchange_code_for_tokens(*, settings, code, redirect_uri, client):
-        return {"access_token": "provider-access", "refresh_token": "provider-refresh"}
-
-    def fake_verify_provider_access_token(*, settings, token, jwks):
-        return {"sub": "auth-sub-1", "email": "callback@headquarter.local", "name": "Callback User"}
-
-    async def fake_fetch_jwks(*, settings, client):
-        return {"keys": []}
-
-    monkeypatch.setattr("src.api.auth.exchange_code_for_tokens", fake_exchange_code_for_tokens)
-    monkeypatch.setattr("src.api.auth.verify_provider_access_token", fake_verify_provider_access_token)
-    monkeypatch.setattr("src.api.auth.fetch_jwks", fake_fetch_jwks)
-
-    client = TestClient(app)
-    client.cookies.set("auth_state", "good-state")
-    response = client.get("/auth/callback?code=valid-code&state=good-state")
-
-    assert response.status_code == 200
-    assert response.json()["email"] == "callback@headquarter.local"
-    set_cookie_header = response.headers.get("set-cookie", "")
-    assert "access_token=" in set_cookie_header
-    assert "refresh_token=" in set_cookie_header
-
-
-@pytest.mark.integration
-def test_refresh_rotates_cookie_and_returns_user_payload(monkeypatch) -> None:
-    _prepare_auth_test_db()
-    _insert_user_for_refresh("7f4b7ad8-c4ce-4d1b-8c83-7ce0f4f66dfb")
-    app = _load_app()
-
-    async def fake_rotate_refresh_token(*, session, raw_token, user_agent, ip_address):
-        class StoredToken:
-            user_id = uuid.UUID("7f4b7ad8-c4ce-4d1b-8c83-7ce0f4f66dfb")
-
-        return "new-refresh-token", StoredToken()
-
-    monkeypatch.setattr("src.api.auth.rotate_refresh_token", fake_rotate_refresh_token)
-
-    client = TestClient(app)
-    client.cookies.set("refresh_token", "old-refresh-token")
-    response = client.post("/auth/refresh")
-
-    assert response.status_code == 200
-    assert response.json()["sub"] == "7f4b7ad8-c4ce-4d1b-8c83-7ce0f4f66dfb"
-    assert "refresh_token=" in response.headers.get("set-cookie", "")
-
-
-@pytest.mark.integration
-def test_refresh_returns_401_for_invalid_refresh_token(monkeypatch) -> None:
-    _prepare_auth_test_db()
-    app = _load_app()
-
-    async def fake_rotate_refresh_token(*, session, raw_token, user_agent, ip_address):
-        raise ValueError("refresh token not found")
-
-    monkeypatch.setattr("src.api.auth.rotate_refresh_token", fake_rotate_refresh_token)
-
-    client = TestClient(app)
-    client.cookies.set("refresh_token", "invalid")
-    response = client.post("/auth/refresh")
-
-    assert response.status_code == 401
+    # Check that session cookie is deleted
+    set_cookie = response.headers.get("set-cookie", "")
+    assert "session=" in set_cookie or "session=\"\"" in set_cookie

apps/api/tests/integration/test_auth_services.py

@@ -1,16 +1,9 @@
-from datetime import UTC, datetime, timedelta
-import base64
-
-import httpx
 import pytest
-from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.cookies import build_cookie_options
-from src.auth.jwt_service import decode_access_token, mint_access_token
-from src.auth.oidc import build_login_redirect_url, exchange_code_for_tokens, verify_provider_access_token
-from src.auth.refresh_store import create_refresh_token, hash_refresh_token, revoke_refresh_token, rotate_refresh_token
+from src.auth.oidc import build_login_redirect_url
+from src.auth.session import create_session_cookie, decode_session_cookie
 from src.config import Settings
-from src.models.user import User
 
 
 @pytest.mark.integration
@@ -38,153 +31,44 @@ def test_login_redirect_url_contains_required_oidc_params() -> None:
         settings=settings,
         redirect_uri="http://localhost:8000/auth/callback",
         state="state-123",
-        nonce="nonce-123",
     )
 
     assert "response_type=code" in url
     assert "client_id=headquarter-web" in url
     assert "scope=openid+profile+email" in url
     assert "state=state-123" in url
-    assert "nonce=nonce-123" in url
 
 
 @pytest.mark.integration
-def test_mint_and_decode_internal_access_token_round_trip() -> None:
+def test_create_and_decode_session_cookie_round_trip() -> None:
     settings = Settings()
-    expires_at = datetime.now(UTC) + timedelta(minutes=15)
+    user_id = "test-user-123"
 
-    token = mint_access_token(
-        settings=settings,
-        subject="user-123",
-        email="dev@headquarter.local",
-        name="Dev User",
-        expires_at=expires_at,
-    )
+    cookie = create_session_cookie(settings=settings, user_id=user_id)
+    payload = decode_session_cookie(settings=settings, cookie_value=cookie)
 
-    claims = decode_access_token(settings=settings, token=token)
-
-    assert claims["sub"] == "user-123"
-    assert claims["email"] == "dev@headquarter.local"
-    assert claims["name"] == "Dev User"
-    assert "exp" in claims
+    assert payload["user_id"] == user_id
+    assert "exp" in payload
 
 
 @pytest.mark.integration
-def test_refresh_token_hash_is_deterministic_and_non_reversible() -> None:
-    raw_token = "refresh-token-abc"
-
-    first_hash = hash_refresh_token(raw_token)
-    second_hash = hash_refresh_token(raw_token)
-
-    assert first_hash == second_hash
-    assert first_hash != raw_token
-    assert len(first_hash) == 64
-
-
-@pytest.mark.integration
-def test_decode_access_token_rejects_invalid_signature() -> None:
+def test_decode_session_rejects_invalid_signature() -> None:
     settings = Settings()
-    other_settings = Settings(jwt_secret="different-secret")
-    expires_at = datetime.now(UTC) + timedelta(minutes=15)
+    other_settings = Settings(session_secret="different-secret")
+    user_id = "test-user-123"
 
-    token = mint_access_token(
-        settings=other_settings,
-        subject="user-123",
-        email="dev@headquarter.local",
-        name="Dev User",
-        expires_at=expires_at,
-    )
+    cookie = create_session_cookie(settings=other_settings, user_id=user_id)
 
-    with pytest.raises(Exception):
-        decode_access_token(settings=settings, token=token)
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_exchange_code_for_tokens_posts_expected_payload() -> None:
-    settings = Settings()
-
-    def handler(request: httpx.Request) -> httpx.Response:
-        assert request.url == httpx.URL(settings.resolved_authentik_token_url)
-        payload = dict(httpx.QueryParams(request.content.decode("utf-8")))
-        assert payload["grant_type"] == "authorization_code"
-        assert payload["code"] == "auth-code"
-        assert payload["redirect_uri"] == "http://localhost:8000/auth/callback"
-        return httpx.Response(200, json={"access_token": "provider-token", "refresh_token": "provider-refresh"})
-
-    transport = httpx.MockTransport(handler)
-    async with httpx.AsyncClient(transport=transport) as client:
-        token_payload = await exchange_code_for_tokens(
-            settings=settings,
-            code="auth-code",
-            redirect_uri="http://localhost:8000/auth/callback",
-            client=client,
-        )
-
-    assert token_payload["access_token"] == "provider-token"
+    with pytest.raises(ValueError, match="invalid session signature"):
+        decode_session_cookie(settings=settings, cookie_value=cookie)
 
 
 @pytest.mark.integration
-def test_verify_provider_access_token_with_jwks_oct_key() -> None:
-    settings = Settings(authentik_audience="headquarter-web", authentik_issuer="https://authentik.local/")
-    shared_secret = b"shared-secret-123"
-    jwks = {
-        "keys": [
-            {
-                "kty": "oct",
-                "alg": "HS256",
-                "k": base64.urlsafe_b64encode(shared_secret).decode("utf-8").rstrip("="),
-                "kid": "kid-1",
-            }
-        ]
-    }
+def test_decode_session_rejects_expired_cookie(monkeypatch) -> None:
+    settings = Settings(session_ttl_hours=-1)  # Already expired
+    user_id = "test-user-123"
 
-    from jose import jwt  # type: ignore[import-untyped]
+    cookie = create_session_cookie(settings=settings, user_id=user_id)
 
-    token = jwt.encode(
-        {
-            "sub": "authentik-user",
-            "iss": settings.authentik_issuer,
-            "aud": settings.authentik_audience,
-            "exp": int((datetime.now(UTC) + timedelta(minutes=5)).timestamp()),
-        },
-        shared_secret,
-        algorithm="HS256",
-        headers={"kid": "kid-1"},
-    )
-
-    claims = verify_provider_access_token(settings=settings, token=token, jwks=jwks)
-
-    assert claims["sub"] == "authentik-user"
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_refresh_store_create_rotate_and_revoke(db_session: AsyncSession) -> None:
-    user = User(email="dev-auth@headquarter.local", name="Dev Auth", authentik_id="auth-dev", avatar_url=None)
-    db_session.add(user)
-    await db_session.commit()
-    await db_session.refresh(user)
-
-    raw_refresh_token, stored_token = await create_refresh_token(
-        session=db_session,
-        user_id=user.id,
-        expires_at=datetime.now(UTC) + timedelta(days=7),
-        user_agent="pytest",
-        ip_address="127.0.0.1",
-    )
-    assert raw_refresh_token
-    assert stored_token.revoked_at is None
-
-    rotated_raw, rotated_stored = await rotate_refresh_token(
-        session=db_session,
-        raw_token=raw_refresh_token,
-        user_agent="pytest-rotated",
-        ip_address="127.0.0.2",
-    )
-    assert rotated_raw != raw_refresh_token
-    assert rotated_stored.revoked_at is None
-    assert stored_token.revoked_at is not None
-
-    revoked = await revoke_refresh_token(session=db_session, raw_token=rotated_raw)
-    assert revoked is True
+    with pytest.raises(ValueError, match="session expired"):
+        decode_session_cookie(settings=settings, cookie_value=cookie)

apps/api/tests/integration/test_config_folders_api.py

@@ -0,0 +1,255 @@
+import uuid
+import pytest
+from fastapi.testclient import TestClient
+
+
+@pytest.mark.integration
+class TestConfigFoldersAPI:
+    """Integration tests for config folders API."""
+
+    def test_list_config_folders_requires_authentication(self, test_client: TestClient) -> None:
+        """Test that listing config folders requires authentication."""
+        response = test_client.get("/config-folders")
+        assert response.status_code == 401
+
+    def test_list_config_folders_returns_user_folders(self, authenticated_client: TestClient) -> None:
+        """Test that authenticated users can list their folders."""
+        response = authenticated_client.get("/config-folders")
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, dict)
+        assert "folders" in data
+        assert isinstance(data["folders"], list)
+
+    def test_create_config_folder_successfully(self, authenticated_client: TestClient) -> None:
+        """Test creating a config folder."""
+        response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "test-folder",
+                "description": "Test folder",
+                "mount_path": "/home/user",
+                "files": {"test.txt": "hello world"},
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["name"] == "test-folder"
+        assert data["mount_path"] == "/home/user"
+        assert data["files"] == {"test.txt": "hello world"}
+
+    def test_create_config_folder_duplicate_name(self, authenticated_client: TestClient) -> None:
+        """Test that duplicate folder names are rejected."""
+        # Create first folder
+        response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "duplicate-folder",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        assert response.status_code == 201
+
+        # Try to create second with same name
+        response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "duplicate-folder",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        assert response.status_code == 409
+
+    def test_create_config_folder_exceeds_size_limit(self, authenticated_client: TestClient) -> None:
+        """Test that folders exceeding 10MB are rejected."""
+        large_content = "x" * (11 * 1024 * 1024)  # 11MB
+        response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "large-folder",
+                "mount_path": "/home/user",
+                "files": {"large.txt": large_content},
+            },
+        )
+        assert response.status_code == 422
+
+    def test_create_config_folder_path_traversal_attack(self, authenticated_client: TestClient) -> None:
+        """Test that path traversal in file paths is prevented."""
+        response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "bad-folder",
+                "mount_path": "/home/user",
+                "files": {"../../../etc/passwd": "malicious"},
+            },
+        )
+        assert response.status_code == 422
+
+    def test_get_config_folder_by_id(self, authenticated_client: TestClient) -> None:
+        """Test getting a config folder by ID."""
+        # Create folder first
+        create_response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "get-test",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        folder_id = create_response.json()["id"]
+
+        # Get it back
+        response = authenticated_client.get(f"/config-folders/{folder_id}")
+        assert response.status_code == 200
+        data = response.json()
+        assert data["name"] == "get-test"
+
+    def test_get_config_folder_not_found(self, authenticated_client: TestClient) -> None:
+        """Test getting a non-existent folder."""
+        response = authenticated_client.get(f"/config-folders/{uuid.uuid4()}")
+        assert response.status_code == 404
+
+    def test_update_config_folder_successfully(self, authenticated_client: TestClient) -> None:
+        """Test updating a config folder."""
+        # Create folder first
+        create_response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "update-test",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        folder_id = create_response.json()["id"]
+
+        # Update it
+        response = authenticated_client.put(
+            f"/config-folders/{folder_id}",
+            json={
+                "name": "updated-name",
+                "mount_path": "/workspace",
+                "files": {"new.txt": "content"},
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["name"] == "updated-name"
+        assert data["mount_path"] == "/workspace"
+
+    def test_delete_config_folder_successfully(self, authenticated_client: TestClient) -> None:
+        """Test deleting a config folder."""
+        # Create folder first
+        create_response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "delete-test",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        folder_id = create_response.json()["id"]
+
+        # Delete it
+        response = authenticated_client.delete(f"/config-folders/{folder_id}")
+        assert response.status_code == 204
+
+        # Verify it's gone
+        get_response = authenticated_client.get(f"/config-folders/{folder_id}")
+        assert get_response.status_code == 404
+
+    def test_add_project_override_successfully(self, authenticated_client: TestClient) -> None:
+        """Test adding a project override."""
+        # Create folder first
+        create_response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "override-test",
+                "mount_path": "/home/user",
+                "files": {"global.txt": "global"},
+            },
+        )
+        folder_id = create_response.json()["id"]
+        project_id = str(uuid.uuid4())
+
+        # Add override
+        response = authenticated_client.post(
+            f"/config-folders/{folder_id}/overrides",
+            json={
+                "project_id": project_id,
+                "mount_path": "/workspace",
+                "files": {"project.txt": "project"},
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert project_id in data["project_overrides"]
+
+    def test_update_project_override_successfully(self, authenticated_client: TestClient) -> None:
+        """Test updating a project override."""
+        # Create folder with override
+        create_response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "update-override-test",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        folder_id = create_response.json()["id"]
+        project_id = str(uuid.uuid4())
+
+        # Add override
+        authenticated_client.post(
+            f"/config-folders/{folder_id}/overrides",
+            json={
+                "project_id": project_id,
+                "mount_path": "/workspace",
+                "files": {"old.txt": "old"},
+            },
+        )
+
+        # Update override
+        response = authenticated_client.put(
+            f"/config-folders/{folder_id}/overrides/{project_id}",
+            json={
+                "mount_path": "/app",
+                "files": {"new.txt": "new"},
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["project_overrides"][project_id]["mount_path"] == "/app"
+
+    def test_delete_project_override_successfully(self, authenticated_client: TestClient) -> None:
+        """Test deleting a project override."""
+        # Create folder with override
+        create_response = authenticated_client.post(
+            "/config-folders",
+            json={
+                "name": "delete-override-test",
+                "mount_path": "/home/user",
+                "files": {},
+            },
+        )
+        folder_id = create_response.json()["id"]
+        project_id = str(uuid.uuid4())
+
+        # Add override
+        authenticated_client.post(
+            f"/config-folders/{folder_id}/overrides",
+            json={
+                "project_id": project_id,
+                "mount_path": "/workspace",
+                "files": {},
+            },
+        )
+
+        # Delete override
+        response = authenticated_client.delete(
+            f"/config-folders/{folder_id}/overrides/{project_id}"
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert project_id not in data["project_overrides"]

apps/api/tests/integration/test_git_control.py

@@ -0,0 +1,150 @@
+"""Tests for git control utilities."""
+
+import os
+import tempfile
+
+import pytest
+
+from src.utils.git_control import (
+    GitStatus,
+    checkout_branch,
+    commit_changes,
+    create_branch,
+    delete_branch,
+    get_current_branch,
+    get_status,
+)
+
+
+@pytest.fixture
+def temp_repo():
+    """Create a temporary git repository."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Initialize git repo
+        os.system(f"cd {tmpdir} && git init && git config user.email 'test@test.com' && git config user.name 'Test User'")
+        
+        # Create initial commit
+        with open(os.path.join(tmpdir, "README.md"), "w") as f:
+            f.write("# Test Repo\n")
+        os.system(f"cd {tmpdir} && git add README.md && git commit -m 'Initial commit'")
+        
+        yield tmpdir
+
+
+class TestGitStatus:
+    """Tests for get_status function."""
+
+    def test_clean_repo(self, temp_repo):
+        """Test status of a clean repository."""
+        status = get_status(temp_repo)
+        assert isinstance(status, GitStatus)
+        assert status.branch in ["main", "master"]
+        assert len(status.modified) == 0
+        assert len(status.added) == 0
+        assert len(status.deleted) == 0
+        assert len(status.untracked) == 0
+
+    def test_modified_file(self, temp_repo):
+        """Test detecting modified files."""
+        # Modify a file
+        with open(os.path.join(temp_repo, "README.md"), "w") as f:
+            f.write("# Modified\n")
+        
+        status = get_status(temp_repo)
+        assert "README.md" in status.modified
+
+    def test_untracked_file(self, temp_repo):
+        """Test detecting untracked files."""
+        # Create new file
+        with open(os.path.join(temp_repo, "new.py"), "w") as f:
+            f.write("print('hello')\n")
+        
+        status = get_status(temp_repo)
+        assert "new.py" in status.untracked
+
+
+def test_get_current_branch_handles_unborn_main() -> None:
+    with tempfile.TemporaryDirectory() as tmpdir:
+        os.system(f"git init -b main {tmpdir} >/dev/null 2>&1")
+
+        assert get_current_branch(tmpdir) == "main"
+
+
+class TestBranchOperations:
+    """Tests for branch management functions."""
+
+    def test_create_branch(self, temp_repo):
+        """Test creating a new branch."""
+        # Get the actual default branch name
+        default_branch = get_current_branch(temp_repo)
+        create_branch(temp_repo, "feature/test", default_branch)
+        
+        # Check branch exists
+        branches = get_status(temp_repo)
+        # Branch should still be on default
+        assert branches.branch == default_branch
+
+    def test_checkout_branch(self, temp_repo):
+        """Test checking out a branch."""
+        default_branch = get_current_branch(temp_repo)
+        create_branch(temp_repo, "feature/test", default_branch)
+        checkout_branch(temp_repo, "feature/test")
+        
+        current = get_current_branch(temp_repo)
+        assert current == "feature/test"
+
+    def test_delete_branch(self, temp_repo):
+        """Test deleting a branch."""
+        default_branch = get_current_branch(temp_repo)
+        create_branch(temp_repo, "feature/delete", default_branch)
+        delete_branch(temp_repo, "feature/delete")
+        
+        # Should be back on default
+        current = get_current_branch(temp_repo)
+        assert current == default_branch
+
+    def test_get_current_branch(self, temp_repo):
+        """Test getting current branch."""
+        branch = get_current_branch(temp_repo)
+        assert branch in ["main", "master"]
+
+
+class TestCommit:
+    """Tests for commit function."""
+
+    def test_commit_changes(self, temp_repo):
+        """Test committing changes."""
+        # Modify file
+        with open(os.path.join(temp_repo, "README.md"), "w") as f:
+            f.write("# Updated\n")
+        
+        # Commit
+        commit_changes(
+            temp_repo,
+            "Update README",
+            "Test User",
+            "test@test.com",
+            ["README.md"]
+        )
+        
+        # Check status is clean
+        status = get_status(temp_repo)
+        assert "README.md" not in status.modified
+
+    def test_commit_all_changes(self, temp_repo):
+        """Test committing all changes."""
+        # Modify file
+        with open(os.path.join(temp_repo, "README.md"), "w") as f:
+            f.write("# All updated\n")
+        
+        # Commit all
+        commit_changes(
+            temp_repo,
+            "Update all",
+            "Test User",
+            "test@test.com"
+        )
+        
+        # Check status is clean
+        status = get_status(temp_repo)
+        assert len(status.modified) == 0

apps/api/tests/integration/test_models.py

@@ -5,7 +5,6 @@ from src.models import Base
 from src.models.base import TimestampMixin, UUIDPrimaryKeyMixin
 from src.models.git_repository import GitRepository
 from src.models.project import Project
-from src.models.refresh_token import RefreshToken
 from src.models.ssh_key import SSHKey
 from src.models.user import User
 from src.models.user_config import UserConfig

apps/api/tests/integration/test_projects_api.py

@@ -6,7 +6,7 @@ import pytest
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import create_async_engine, async_sessionmaker
 
-from src.auth.jwt_service import mint_access_token
+from src.auth.session import create_session_cookie
 from src.config import Settings, build_database_url
 from src.models import Base
 from src.models.project import Project
@@ -53,7 +53,7 @@ def _load_app():
 
 def _mint_token(user_id: str) -> str:
     settings = Settings()
-    return mint_access_token(
+    return create_session_cookie(
         settings=settings,
         subject=user_id,
         email="test@headquarter.local",

apps/api/tests/integration/test_tool_configs_api_extended.py

@@ -0,0 +1,256 @@
+import uuid
+import pytest
+from fastapi.testclient import TestClient
+
+
+@pytest.mark.integration
+class TestToolConfigsAPIExtended:
+    """Integration tests for tool configs API with new fields."""
+
+    def test_create_tool_config_with_new_fields(self, authenticated_client: TestClient) -> None:
+        """Test creating a tool config with all new fields."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "config-test-tool",
+                "display_name": "Config Test Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Create config with new fields
+        response = authenticated_client.post(
+            "/tool-configs",
+            json={
+                "tool_type_id": tool_id,
+                "key": "ADVANCED_CONFIG",
+                "value": "test-value",
+                "config_type": "env",
+                "port_override": 9090,
+                "start_command": "python app.py",
+                "working_directory": "/app",
+                "environment_variables": {"DEBUG": "true", "LOG_LEVEL": "debug"},
+                "volumes": [
+                    {"source": "data", "target": "/data", "type": "bind"}
+                ],
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["key"] == "ADVANCED_CONFIG"
+        assert data["port_override"] == 9090
+        assert data["start_command"] == "python app.py"
+        assert data["working_directory"] == "/app"
+        assert data["environment_variables"] == {"DEBUG": "true", "LOG_LEVEL": "debug"}
+        assert data["volumes"] == [{"source": "data", "target": "/data", "type": "bind"}]
+
+    def test_create_tool_config_invalid_port(self, authenticated_client: TestClient) -> None:
+        """Test that invalid port numbers are rejected."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "port-test-tool",
+                "display_name": "Port Test Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Try to create config with invalid port
+        response = authenticated_client.post(
+            "/tool-configs",
+            json={
+                "tool_type_id": tool_id,
+                "key": "BAD_PORT",
+                "value": "test",
+                "config_type": "env",
+                "port_override": 99999,
+            },
+        )
+        assert response.status_code == 422
+
+    def test_create_tool_config_invalid_volume_structure(self, authenticated_client: TestClient) -> None:
+        """Test that invalid volume structures are rejected."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "volume-test-tool",
+                "display_name": "Volume Test Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Try to create config with invalid volume
+        response = authenticated_client.post(
+            "/tool-configs",
+            json={
+                "tool_type_id": tool_id,
+                "key": "BAD_VOLUME",
+                "value": "test",
+                "config_type": "env",
+                "volumes": [{"invalid": "structure"}],
+            },
+        )
+        assert response.status_code == 422
+
+    def test_update_tool_config_with_new_fields(self, authenticated_client: TestClient) -> None:
+        """Test updating a tool config with new fields."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "update-config-tool",
+                "display_name": "Update Config Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Create config
+        create_response = authenticated_client.post(
+            "/tool-configs",
+            json={
+                "tool_type_id": tool_id,
+                "key": "UPDATE_TEST",
+                "value": "original",
+                "config_type": "env",
+            },
+        )
+        config_id = create_response.json()["id"]
+
+        # Update with new fields
+        response = authenticated_client.put(
+            f"/tool-configs/{config_id}",
+            json={
+                "value": "updated",
+                "port_override": 3000,
+                "start_command": "npm start",
+                "working_directory": "/workspace",
+                "environment_variables": {"NODE_ENV": "production"},
+                "volumes": [{"source": "src", "target": "/app/src", "type": "bind"}],
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["value"] == "updated"
+        assert data["port_override"] == 3000
+        assert data["start_command"] == "npm start"
+        assert data["working_directory"] == "/workspace"
+        assert data["environment_variables"] == {"NODE_ENV": "production"}
+
+    def test_list_tool_configs_returns_new_fields(self, authenticated_client: TestClient) -> None:
+        """Test that listing configs returns new fields."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "list-config-tool",
+                "display_name": "List Config Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Create config with new fields
+        authenticated_client.post(
+            "/tool-configs",
+            json={
+                "tool_type_id": tool_id,
+                "key": "LIST_TEST",
+                "value": "test",
+                "config_type": "env",
+                "port_override": 5000,
+                "environment_variables": {"TEST": "true"},
+            },
+        )
+
+        # List configs
+        response = authenticated_client.get("/tool-configs")
+        assert response.status_code == 200
+        data = response.json()
+        assert len(data) > 0
+        config = data[0]
+        assert "port_override" in config
+        assert "start_command" in config
+        assert "working_directory" in config
+        assert "environment_variables" in config
+        assert "volumes" in config
+
+    def test_get_tool_config_defaults(self, authenticated_client: TestClient) -> None:
+        """Test getting tool config defaults."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "defaults-tool",
+                "display_name": "Defaults Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx\n    volumes:\n      - \"{{REPO_PATH}}:/workspace\"\n",
+                "required_variables": ["REPO_PATH"],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Get defaults
+        response = authenticated_client.get(f"/tool-configs/defaults/{tool_id}")
+        assert response.status_code == 200
+        data = response.json()
+        assert data["tool_type_id"] == tool_id
+        assert "suggested_configs" in data
+
+    def test_tool_config_backward_compatibility(self, authenticated_client: TestClient) -> None:
+        """Test that old configs without new fields still work."""
+        # Create a tool type first
+        tool_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "backward-compat-tool",
+                "display_name": "Backward Compat Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = tool_response.json()["id"]
+
+        # Create config without new fields (simulating old client)
+        response = authenticated_client.post(
+            "/tool-configs",
+            json={
+                "tool_type_id": tool_id,
+                "key": "OLD_STYLE",
+                "value": "value",
+                "config_type": "env",
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["key"] == "OLD_STYLE"
+        # New fields should have default values
+        assert data["port_override"] is None
+        assert data["start_command"] is None
+        assert data["working_directory"] is None
+        assert data["environment_variables"] is None
+        assert data["volumes"] is None

apps/api/tests/integration/test_tool_types_api.py

@@ -7,7 +7,7 @@ from fastapi.testclient import TestClient
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import create_async_engine, async_sessionmaker
 
-from src.auth.jwt_service import mint_access_token
+from src.auth.session import create_session_cookie
 from src.config import Settings, build_database_url
 from src.models import Base
 from src.models.tool_type import ToolType
@@ -54,7 +54,7 @@ def _load_app():
 
 def _mint_token(user_id: str) -> str:
     settings = Settings()
-    return mint_access_token(
+    return create_session_cookie(
         settings=settings,
         subject=user_id,
         email="test@headquarter.local",

apps/api/tests/integration/test_tool_types_api_extended.py

@@ -0,0 +1,188 @@
+import uuid
+import pytest
+from fastapi.testclient import TestClient
+
+
+@pytest.mark.integration
+class TestToolTypesAPIExtended:
+    """Integration tests for tool types API with new fields."""
+
+    def test_create_tool_type_with_dockerfile(self, authenticated_client: TestClient) -> None:
+        """Test creating a tool type with dockerfile definition."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "dockerfile-tool",
+                "display_name": "Dockerfile Tool",
+                "category": "utility",
+                "interfaces": ["terminal"],
+                "default_port": 8080,
+                "definition_type": "dockerfile",
+                "dockerfile_template": "FROM python:3.11\nRUN pip install flask",
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["name"] == "dockerfile-tool"
+        assert data["definition_type"] == "dockerfile"
+        assert data["dockerfile_template"] == "FROM python:3.11\nRUN pip install flask"
+
+    def test_create_tool_type_with_readiness_probe(self, authenticated_client: TestClient) -> None:
+        """Test creating a tool type with readiness probe."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "probed-tool",
+                "display_name": "Probed Tool",
+                "category": "utility",
+                "interfaces": ["web"],
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "readiness_probe": {
+                    "command": "curl -f http://localhost:8080",
+                    "timeout": 30,
+                    "interval": 2,
+                },
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["readiness_probe"]["command"] == "curl -f http://localhost:8080"
+        assert data["readiness_probe"]["timeout"] == 30
+
+    def test_create_tool_type_invalid_definition_type(self, authenticated_client: TestClient) -> None:
+        """Test that invalid definition types are rejected."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "invalid-tool",
+                "display_name": "Invalid Tool",
+                "default_port": 8080,
+                "definition_type": "invalid",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 422
+
+    def test_create_tool_type_dockerfile_without_template(self, authenticated_client: TestClient) -> None:
+        """Test that dockerfile type requires dockerfile_template."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "no-dockerfile",
+                "display_name": "No Dockerfile",
+                "default_port": 8080,
+                "definition_type": "dockerfile",
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 422
+
+    def test_update_tool_type_with_new_fields(self, authenticated_client: TestClient) -> None:
+        """Test updating a tool type with new fields."""
+        # Create tool type first
+        create_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "update-test-tool",
+                "display_name": "Update Test Tool",
+                "default_port": 8080,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "required_variables": [],
+            },
+        )
+        tool_id = create_response.json()["id"]
+
+        # Update it
+        response = authenticated_client.put(
+            f"/tool-types/{tool_id}",
+            json={
+                "display_name": "Updated Name",
+                "readiness_probe": {
+                    "command": "curl -f http://localhost:8080/health",
+                    "timeout": 60,
+                    "interval": 5,
+                },
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["display_name"] == "Updated Name"
+        assert data["readiness_probe"]["command"] == "curl -f http://localhost:8080/health"
+
+    def test_validate_tool_type_compose(self, authenticated_client: TestClient) -> None:
+        """Test validating compose template."""
+        response = authenticated_client.post(
+            "/tool-types/validate",
+            json={
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["valid"] is True
+
+    def test_validate_tool_type_invalid_compose(self, authenticated_client: TestClient) -> None:
+        """Test validating invalid compose template."""
+        response = authenticated_client.post(
+            "/tool-types/validate",
+            json={
+                "definition_type": "compose",
+                "compose_template": "invalid: yaml: [",
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["valid"] is False
+        assert "errors" in data
+
+    def test_validate_tool_type_dockerfile(self, authenticated_client: TestClient) -> None:
+        """Test validating dockerfile template."""
+        response = authenticated_client.post(
+            "/tool-types/validate",
+            json={
+                "definition_type": "dockerfile",
+                "dockerfile_template": "FROM python:3.11\nRUN pip install flask",
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["valid"] is True
+
+    def test_get_tool_type_returns_new_fields(self, authenticated_client: TestClient) -> None:
+        """Test that GET returns new fields."""
+        # Create tool type with all fields
+        create_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "full-tool",
+                "display_name": "Full Tool",
+                "category": "editor",
+                "interfaces": ["web", "terminal"],
+                "default_port": 8443,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: code-server\n    volumes:\n      - \"{{REPO_PATH}}:/workspace\"",
+                "readiness_probe": {
+                    "command": "curl -f http://localhost:8443",
+                    "timeout": 30,
+                    "interval": 2,
+                },
+                "required_variables": ["REPO_PATH"],
+            },
+        )
+        tool_id = create_response.json()["id"]
+
+        # Get it
+        response = authenticated_client.get(f"/tool-types/{tool_id}")
+        assert response.status_code == 200
+        data = response.json()
+        assert data["definition_type"] == "compose"
+        assert data["category"] == "editor"
+        assert data["interfaces"] == ["web", "terminal"]
+        assert "readiness_probe" in data

apps/api/tests/integration/test_users_api.py

@@ -8,7 +8,7 @@ import pytest
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import create_async_engine
 
-from src.auth.jwt_service import mint_access_token
+from src.auth.session import create_session_cookie
 from src.config import Settings, build_database_url
 from src.models import Base
 from src.models.user import User
@@ -78,7 +78,7 @@ def _insert_test_user(user_id: str) -> None:
 
 def _create_auth_cookie(user_id: str) -> str:
     settings = Settings()
-    return mint_access_token(
+    return create_session_cookie(
         settings=settings,
         subject=user_id,
         email="test@headquarter.local",

apps/api/tests/unit/test_docker_build.py

@@ -0,0 +1,151 @@
+"""Unit tests for docker build service."""
+
+import subprocess
+import tempfile
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from src.services.docker_build import build_image
+
+
+class TestBuildImage:
+    """Tests for build_image function."""
+
+    @patch("subprocess.run")
+    def test_builds_image_successfully(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="Successfully built abc123",
+            stderr="",
+        )
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = build_image(tmpdir, "FROM python:3.11", "test-image:latest")
+            
+            assert result[0] == 0
+            assert "Successfully built" in result[1]
+            mock_run.assert_called_once()
+            call_args = mock_run.call_args
+            assert "test-image:latest" in call_args[0][0]
+            assert "build" in call_args[0][0]
+
+    @patch("subprocess.run")
+    def test_build_fails(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=1,
+            stdout="",
+            stderr="Error: failed to build",
+        )
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = build_image(tmpdir, "FROM invalid:image", "test-image:latest")
+            
+            assert result[0] == 1
+            assert "failed to build" in result[2]
+
+    @patch("subprocess.run")
+    def test_build_with_tag(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="",
+            stderr="",
+        )
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            build_image(tmpdir, "FROM python:3.11", "my-registry/tool:v1.0")
+            
+            call_args = mock_run.call_args[0][0]
+            assert "my-registry/tool:v1.0" in call_args
+
+    @patch("subprocess.run")
+    def test_build_command_structure(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            build_image(tmpdir, "FROM python:3.11", "test:latest")
+            
+            cmd = mock_run.call_args[0][0]
+            assert cmd[0] == "docker"
+            assert cmd[1] == "build"
+            assert "-t" in cmd
+            assert "test:latest" in cmd
+            assert tmpdir in cmd
+
+    @patch("subprocess.run")
+    def test_build_writes_dockerfile(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            dockerfile_content = "FROM python:3.11\\nRUN pip install flask"
+            build_image(tmpdir, dockerfile_content, "test:latest")
+            
+            dockerfile_path = Path(tmpdir) / "Dockerfile"
+            assert dockerfile_path.exists()
+            assert dockerfile_path.read_text() == dockerfile_content
+
+    @patch("subprocess.run")
+    def test_build_writes_context_files(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            build_context = {
+                "requirements.txt": "flask==2.0\\nnumpy==1.21",
+                "app.py": "from flask import Flask\\napp = Flask(__name__)",
+            }
+            build_image(tmpdir, "FROM python:3.11", "test:latest", build_context)
+            
+            req_path = Path(tmpdir) / "requirements.txt"
+            app_path = Path(tmpdir) / "app.py"
+            assert req_path.exists()
+            assert req_path.read_text() == "flask==2.0\\nnumpy==1.21"
+            assert app_path.exists()
+            assert app_path.read_text() == "from flask import Flask\\napp = Flask(__name__)"
+
+    @patch("subprocess.run")
+    def test_build_creates_nested_directories(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            build_context = {
+                "src/app.py": "print('hello')",
+            }
+            build_image(tmpdir, "FROM python:3.11", "test:latest", build_context)
+            
+            app_path = Path(tmpdir) / "src" / "app.py"
+            assert app_path.exists()
+
+    @patch("subprocess.run")
+    def test_build_prevents_path_traversal(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            build_context = {
+                "../../../etc/passwd": "root:x:0:0",
+            }
+            
+            with pytest.raises(ValueError, match="escapes instance directory"):
+                build_image(tmpdir, "FROM python:3.11", "test:latest", build_context)
+            
+            mock_run.assert_not_called()
+
+    @patch("subprocess.run")
+    def test_build_timeout(self, mock_run) -> None:
+        mock_run.side_effect = subprocess.TimeoutExpired(cmd=["docker", "build"], timeout=300)
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = build_image(tmpdir, "FROM python:3.11", "test:latest")
+            
+            assert result[0] == 1
+            assert "timed out" in result[2].lower()
+
+    @patch("subprocess.run")
+    def test_build_exception(self, mock_run) -> None:
+        mock_run.side_effect = OSError("Docker not available")
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = build_image(tmpdir, "FROM python:3.11", "test:latest")
+            
+            assert result[0] == 1
+            assert "Docker not available" in result[2]

apps/api/tests/unit/test_git_repository_clone_preflight.py

@@ -0,0 +1,28 @@
+from unittest.mock import Mock, patch
+
+import pytest
+from fastapi import HTTPException
+
+from src.api.git_repositories import _build_provider_clone_url, _preflight_remote_repository
+
+
+def test_build_provider_clone_url_uses_fixed_host() -> None:
+    assert _build_provider_clone_url("alice", "demo") == "git@git.commumedia.org:alice/demo.git"
+
+
+def test_preflight_remote_repository_allows_accessible_repo() -> None:
+    completed = Mock(returncode=0)
+    with patch("src.api.git_repositories.subprocess.run", return_value=completed) as run_mock:
+        _preflight_remote_repository("git@git.commumedia.org:alice/demo.git")
+
+    run_mock.assert_called_once()
+
+
+def test_preflight_remote_repository_rejects_missing_repo() -> None:
+    completed = Mock(returncode=128)
+    with patch("src.api.git_repositories.subprocess.run", return_value=completed):
+        with pytest.raises(HTTPException) as exc_info:
+            _preflight_remote_repository("git@git.commumedia.org:alice/missing.git")
+
+    assert exc_info.value.status_code == 400
+    assert exc_info.value.detail == "repository not found or inaccessible"

apps/api/tests/unit/test_git_repository_working_clones.py

@@ -0,0 +1,64 @@
+from unittest.mock import Mock, patch
+
+import pytest
+from fastapi import HTTPException
+
+from src.api.git_repositories import _clone_working_repository, _init_working_repository
+from src.utils.git_control import create_branch
+
+
+def test_clone_working_repository_uses_normal_clone() -> None:
+    completed = Mock(returncode=0, stderr="")
+    with patch("src.api.git_repositories.subprocess.run", return_value=completed) as run_mock:
+        _clone_working_repository("git@git.commumedia.org:alice/demo.git", "/tmp/demo.git")
+
+    run_mock.assert_called_once()
+    assert run_mock.call_args.args[0] == ["git", "clone", "git@git.commumedia.org:alice/demo.git", "/tmp/demo.git"]
+
+
+def test_clone_working_repository_raises_on_failure() -> None:
+    completed = Mock(returncode=128, stderr="fatal: repository not found")
+    with patch("src.api.git_repositories.subprocess.run", return_value=completed):
+        with pytest.raises(HTTPException) as exc_info:
+            _clone_working_repository("git@git.commumedia.org:alice/missing.git", "/tmp/missing.git")
+
+    assert exc_info.value.status_code == 400
+    assert "failed to clone repository" in exc_info.value.detail
+
+
+def test_init_working_repository_prefers_init_b() -> None:
+    init_b = Mock(returncode=0, stderr="")
+    with patch("src.api.git_repositories.subprocess.run", return_value=init_b) as run_mock:
+        _init_working_repository("/tmp/new-repo")
+
+    assert run_mock.call_args.args[0] == ["git", "init", "-b", "main", "/tmp/new-repo"]
+
+
+def test_init_working_repository_falls_back_to_symbolic_ref() -> None:
+    init_b = Mock(returncode=1, stderr="unknown switch `b'")
+    init_ok = Mock(returncode=0, stderr="")
+    symbolic_ref = Mock(returncode=0, stderr="")
+
+    with patch("src.api.git_repositories.subprocess.run", side_effect=[init_b, init_ok, symbolic_ref]) as run_mock:
+        _init_working_repository("/tmp/new-repo")
+
+    assert run_mock.call_args_list[0].args[0] == ["git", "init", "-b", "main", "/tmp/new-repo"]
+    assert run_mock.call_args_list[1].args[0] == ["git", "init", "/tmp/new-repo"]
+    assert run_mock.call_args_list[2].args[0] == ["git", "-C", "/tmp/new-repo", "symbolic-ref", "HEAD", "refs/heads/main"]
+
+
+def test_create_branch_uses_orphan_checkout_when_head_is_unborn() -> None:
+    call_count = 0
+
+    def mock_run(repo_path: str, *args: str) -> str:
+        nonlocal call_count
+        call_count += 1
+        if call_count == 1:
+            raise RuntimeError("fatal: Needed a single revision")
+        return ""
+
+    with patch("src.utils.git_control._run_git_command", side_effect=mock_run) as run_mock:
+        create_branch("/tmp/new-repo", "feature/test")
+
+    assert run_mock.call_args_list[0].args[1:] == ("rev-parse", "--verify", "HEAD^{commit}")
+    assert run_mock.call_args_list[1].args[1:] == ("checkout", "--orphan", "feature/test")

apps/api/tests/unit/test_git_url_parser.py

@@ -0,0 +1,147 @@
+"""Tests for git URL parsing utilities."""
+
+import pytest
+
+from src.utils.git_url_parser import extract_base_repo_url, is_valid_clone_url, parse_git_url
+
+
+class TestExtractBaseRepoUrl:
+    """Tests for extract_base_repo_url function."""
+
+    def test_github_tree_url(self):
+        url = "https://github.com/owner/repo/tree/main"
+        result = extract_base_repo_url(url)
+        assert result == "https://github.com/owner/repo.git"
+
+    def test_github_blob_url(self):
+        url = "https://github.com/owner/repo/blob/main/README.md"
+        result = extract_base_repo_url(url)
+        assert result == "https://github.com/owner/repo.git"
+
+    def test_github_pull_url(self):
+        url = "https://github.com/owner/repo/pull/123"
+        result = extract_base_repo_url(url)
+        assert result == "https://github.com/owner/repo.git"
+
+    def test_github_issues_url(self):
+        url = "https://github.com/owner/repo/issues/456"
+        result = extract_base_repo_url(url)
+        assert result == "https://github.com/owner/repo.git"
+
+    def test_github_valid_url(self):
+        url = "https://github.com/owner/repo.git"
+        result = extract_base_repo_url(url)
+        assert result == "https://github.com/owner/repo.git"
+
+    def test_github_url_with_query_params(self):
+        url = "https://github.com/owner/repo?tab=readme-ov-file"
+        result = extract_base_repo_url(url)
+        assert result == "https://github.com/owner/repo.git"
+
+    def test_gitlab_tree_url(self):
+        url = "https://gitlab.com/owner/repo/-/tree/main"
+        result = extract_base_repo_url(url)
+        assert result == "https://gitlab.com/owner/repo.git"
+
+    def test_gitlab_blob_url(self):
+        url = "https://gitlab.com/owner/repo/-/blob/main/README.md"
+        result = extract_base_repo_url(url)
+        assert result == "https://gitlab.com/owner/repo.git"
+
+    def test_gitlab_merge_request_url(self):
+        url = "https://gitlab.com/owner/repo/-/merge_requests/123"
+        result = extract_base_repo_url(url)
+        assert result == "https://gitlab.com/owner/repo.git"
+
+    def test_gitlab_valid_url(self):
+        url = "https://gitlab.com/owner/repo.git"
+        result = extract_base_repo_url(url)
+        assert result == "https://gitlab.com/owner/repo.git"
+
+    def test_bitbucket_src_url(self):
+        url = "https://bitbucket.org/owner/repo/src/main/"
+        result = extract_base_repo_url(url)
+        assert result == "https://bitbucket.org/owner/repo.git"
+
+    def test_bitbucket_valid_url(self):
+        url = "https://bitbucket.org/owner/repo.git"
+        result = extract_base_repo_url(url)
+        assert result == "https://bitbucket.org/owner/repo.git"
+
+    def test_ssh_url(self):
+        url = "git@github.com:owner/repo.git"
+        result = extract_base_repo_url(url)
+        assert result == "git@github.com:owner/repo.git"
+
+    def test_ssh_url_without_git_suffix(self):
+        url = "git@github.com:owner/repo"
+        result = extract_base_repo_url(url)
+        assert result == "git@github.com:owner/repo.git"
+
+    def test_invalid_url(self):
+        url = "not-a-url"
+        result = extract_base_repo_url(url)
+        assert result is None
+
+    def test_empty_url(self):
+        url = ""
+        result = extract_base_repo_url(url)
+        assert result is None
+
+
+class TestIsValidCloneUrl:
+    """Tests for is_valid_clone_url function."""
+
+    def test_valid_ssh_url(self):
+        assert is_valid_clone_url("git@github.com:owner/repo.git") is True
+
+    def test_valid_https_url(self):
+        assert is_valid_clone_url("https://github.com/owner/repo.git") is True
+
+    def test_browser_url(self):
+        assert is_valid_clone_url("https://github.com/owner/repo/tree/main") is False
+
+    def test_url_without_git_suffix(self):
+        assert is_valid_clone_url("https://github.com/owner/repo") is False
+
+    def test_invalid_url(self):
+        assert is_valid_clone_url("not-a-url") is False
+
+
+class TestParseGitUrl:
+    """Tests for parse_git_url function."""
+
+    def test_valid_git_url(self):
+        result = parse_git_url("https://github.com/owner/repo.git")
+        assert result["is_valid_clone_url"] is True
+        assert result["needs_parsing"] is False
+        assert result["base_url"] == "https://github.com/owner/repo.git"
+        assert result["host"] == "github.com"
+        assert "Valid" in result["message"]
+
+    def test_browser_url(self):
+        result = parse_git_url("https://github.com/owner/repo/tree/main")
+        assert result["is_valid_clone_url"] is False
+        assert result["needs_parsing"] is True
+        assert result["base_url"] == "https://github.com/owner/repo.git"
+        assert result["host"] == "github.com"
+        assert result["error_code"] == "URL_NEEDS_PARSING"
+        assert "browser URL" in result["message"]
+
+    def test_invalid_url(self):
+        result = parse_git_url("not-a-url")
+        assert result["is_valid_clone_url"] is False
+        assert result["base_url"] is None
+        assert result["error_code"] == "INVALID_URL"
+
+    def test_empty_url(self):
+        result = parse_git_url("")
+        assert result["is_valid_clone_url"] is False
+        assert result["base_url"] is None
+        assert result["error_code"] == "INVALID_URL"
+
+    def test_ssh_url(self):
+        result = parse_git_url("git@github.com:owner/repo.git")
+        assert result["is_valid_clone_url"] is True
+        assert result["needs_parsing"] is False
+        assert result["host"] == "github.com"

apps/api/tests/unit/test_migration_metadata.py

@@ -39,3 +39,18 @@ def test_refresh_tokens_migration_has_expected_revision_chain() -> None:
 
     assert module.revision == "0002_refresh_tokens"
     assert module.down_revision == "0001_initial_schema"
+
+
+@pytest.mark.unit
+def test_config_profiles_migration_has_expected_revision_chain() -> None:
+    migration_path = Path(__file__).resolve().parents[2] / "alembic" / "versions" / "0013_add_config_profiles.py"
+    spec = spec_from_file_location("add_config_profiles", migration_path)
+
+    assert spec is not None
+    assert spec.loader is not None
+
+    module = module_from_spec(spec)
+    spec.loader.exec_module(module)
+
+    assert module.revision == "0013_add_config_profiles"
+    assert module.down_revision == "0012_default_port_req"

apps/api/tests/unit/test_readiness_probe.py

@@ -0,0 +1,217 @@
+"""Unit tests for readiness probe service."""
+
+import asyncio
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from src.services.readiness_probe import execute_probe
+
+
+class TestExecuteProbe:
+    """Tests for execute_probe function."""
+
+    @patch("subprocess.run")
+    async def test_probe_succeeds_first_attempt(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="healthy",
+            stderr="",
+        )
+        
+        result, logs = await execute_probe("container-123", "curl -f http://localhost:8080")
+        
+        assert result is True
+        assert any("Success" in log for log in logs)
+        mock_run.assert_called_once_with(
+            ["docker", "exec", "container-123", "sh", "-c", "curl -f http://localhost:8080"],
+            capture_output=True,
+            text=True,
+            timeout=2,
+        )
+
+    @patch("subprocess.run")
+    async def test_probe_fails_then_succeeds(self, mock_run) -> None:
+        mock_run.side_effect = [
+            MagicMock(returncode=1, stdout="", stderr="Connection refused"),
+            MagicMock(returncode=1, stdout="", stderr="Connection refused"),
+            MagicMock(returncode=0, stdout="healthy", stderr=""),
+        ]
+        
+        result, logs = await execute_probe("container-123", "curl -f http://localhost:8080", timeout=10, interval=0.1)
+        
+        assert result is True
+        assert mock_run.call_count == 3
+        assert any("Attempt 1: Failed" in log for log in logs)
+        assert any("Attempt 3: Success" in log for log in logs)
+
+    @patch("subprocess.run")
+    async def test_probe_times_out(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=1,
+            stdout="",
+            stderr="Connection refused",
+        )
+        
+        result, logs = await execute_probe("container-123", "curl -f http://localhost:8080", timeout=0.5, interval=0.2)
+        
+        assert result is False
+        assert any("timed out" in log.lower() for log in logs)
+
+    @patch("subprocess.run")
+    async def test_probe_command_not_found(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=127,
+            stdout="",
+            stderr="command not found",
+        )
+        
+        result, logs = await execute_probe("container-123", "nonexistent-command", timeout=1, interval=0.3)
+        
+        assert result is False
+        assert any("exit code 127" in log for log in logs)
+
+    @patch("subprocess.run")
+    async def test_probe_exception(self, mock_run) -> None:
+        mock_run.side_effect = OSError("Docker not available")
+        
+        result, logs = await execute_probe("container-123", "curl http://localhost", timeout=1, interval=0.3)
+        
+        assert result is False
+        assert any("Error" in log for log in logs)
+
+    @patch("subprocess.run")
+    async def test_probe_with_special_characters(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="",
+            stderr="",
+        )
+        
+        cmd = "bash -c 'echo \"hello world\" && exit 0'"
+        await execute_probe("container-123", cmd)
+        
+        call_args = mock_run.call_args
+        assert cmd in call_args[0][0]
+
+    @patch("subprocess.run")
+    async def test_probe_captures_stdout(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="Server is ready\\nVersion: 1.0",
+            stderr="",
+        )
+        
+        result, logs = await execute_probe("container-123", "cat /app/status")
+        
+        assert result is True
+        assert any("Server is ready" in log for log in logs)
+
+
+class TestIntegrationScenarios:
+    """Integration-style tests with realistic scenarios."""
+
+    @patch("subprocess.run")
+    async def test_web_server_probe(self, mock_run) -> None:
+        """Test typical web server health check."""
+        mock_run.side_effect = [
+            MagicMock(returncode=1, stdout="", stderr=""),
+            MagicMock(returncode=1, stdout="", stderr=""),
+            MagicMock(returncode=1, stdout="", stderr=""),
+            MagicMock(returncode=0, stdout="OK", stderr=""),
+        ]
+        
+        result, logs = await execute_probe(
+            "web-container",
+            "curl -f http://localhost:8080/health",
+            timeout=10,
+            interval=0.2,
+        )
+        
+        assert result is True
+        assert mock_run.call_count == 4
+
+    @patch("subprocess.run")
+    async def test_command_probe(self, mock_run) -> None:
+        """Test command availability check."""
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="opencode 1.0.0",
+            stderr="",
+        )
+        
+        result, logs = await execute_probe(
+            "tool-container",
+            "which opencode && opencode --version",
+            timeout=30,
+            interval=2,
+        )
+        
+        assert result is True
+        assert any("opencode 1.0.0" in log for log in logs)
+
+    @patch("subprocess.run")
+    async def test_database_probe(self, mock_run) -> None:
+        """Test database readiness check."""
+        mock_run.side_effect = [
+            MagicMock(returncode=1, stdout="", stderr=""),
+            MagicMock(returncode=1, stdout="", stderr=""),
+            MagicMock(returncode=0, stdout="/var/run/postgresql:5432 - accepting connections", stderr=""),
+        ]
+        
+        result, logs = await execute_probe(
+            "db-container",
+            "pg_isready -U postgres",
+            timeout=10,
+            interval=0.3,
+        )
+        
+        assert result is True
+        assert mock_run.call_count == 3
+
+    @patch("subprocess.run")
+    async def test_file_probe(self, mock_run) -> None:
+        """Test file existence check."""
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        
+        result, logs = await execute_probe(
+            "app-container",
+            "[ -f /app/ready ]",
+            timeout=10,
+            interval=1,
+        )
+        
+        assert result is True
+
+    @patch("subprocess.run")
+    async def test_slow_starting_service(self, mock_run) -> None:
+        """Test service that takes time to start."""
+        # Simulate 5 failures before success
+        side_effects = [MagicMock(returncode=1, stdout="", stderr="")] * 5
+        side_effects.append(MagicMock(returncode=0, stdout="Ready", stderr=""))
+        mock_run.side_effect = side_effects
+        
+        result, logs = await execute_probe(
+            "slow-container",
+            "curl -f http://localhost:8080",
+            timeout=10,
+            interval=0.2,
+        )
+        
+        assert result is True
+        assert mock_run.call_count == 6
+        assert any("Attempt 6: Success" in log for log in logs)
+
+    @patch("subprocess.run")
+    async def test_zero_timeout_immediate_return(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=1, stdout="", stderr="")
+        
+        result, logs = await execute_probe(
+            "container",
+            "test",
+            timeout=0,
+            interval=1,
+        )
+        
+        assert result is False
+        assert any("timed out" in log.lower() for log in logs)

apps/web/index.html

@@ -4,6 +4,12 @@
     <meta charset="UTF-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Headquarter</title>
+    <link rel="preconnect" href="https://fonts.googleapis.com" />
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
+    <link
+      href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=IBM+Plex+Mono:wght@400;500;600&display=swap"
+      rel="stylesheet"
+    />
   </head>
   <body>
     <div id="root"></div>

apps/web/package-lock.json

@@ -8,11 +8,18 @@
       "name": "headquarter-web",
       "version": "0.1.0",
       "dependencies": {
+        "@phosphor-icons/react": "^2.1.10",
+        "@types/prismjs": "^1.26.6",
         "axios": "^1.6.0",
+        "prismjs": "^1.30.0",
         "react": "^18.2.0",
         "react-dom": "^18.2.0",
         "react-router-dom": "^6.20.0",
-        "tailwindcss": "^3.3.0"
+        "react-simple-code-editor": "^0.14.1",
+        "tailwindcss": "^3.3.0",
+        "xterm": "^5.3.0",
+        "xterm-addon-fit": "^0.8.0",
+        "xterm-addon-web-links": "^0.9.0"
       },
       "devDependencies": {
         "@testing-library/jest-dom": "^6.9.1",
@@ -1268,6 +1275,19 @@
         "url": "https://github.com/sponsors/Boshen"
       }
     },
+    "node_modules/@phosphor-icons/react": {
+      "version": "2.1.10",
+      "resolved": "https://registry.npmjs.org/@phosphor-icons/react/-/react-2.1.10.tgz",
+      "integrity": "sha512-vt8Tvq8GLjheAZZYa+YG/pW7HDbov8El/MANW8pOAz4eGxrwhnbfrQZq0Cp4q8zBEu8NIhHdnr+r8thnfRSNYA==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=10"
+      },
+      "peerDependencies": {
+        "react": ">= 16.8",
+        "react-dom": ">= 16.8"
+      }
+    },
     "node_modules/@remix-run/router": {
       "version": "1.23.2",
       "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.2.tgz",
@@ -2127,6 +2147,12 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/@types/prismjs": {
+      "version": "1.26.6",
+      "resolved": "https://registry.npmjs.org/@types/prismjs/-/prismjs-1.26.6.tgz",
+      "integrity": "sha512-vqlvI7qlMvcCBbVe0AKAb4f97//Hy0EBTaiW8AalRnG/xAN5zOiWWyrNqNXeq8+KAuvRewjCVY1+IPxk4RdNYw==",
+      "license": "MIT"
+    },
     "node_modules/@types/prop-types": {
       "version": "15.7.15",
       "resolved": "https://registry.npmjs.org/@types/prop-types/-/prop-types-15.7.15.tgz",
@@ -5091,6 +5117,15 @@
         "url": "https://github.com/chalk/ansi-styles?sponsor=1"
       }
     },
+    "node_modules/prismjs": {
+      "version": "1.30.0",
+      "resolved": "https://registry.npmjs.org/prismjs/-/prismjs-1.30.0.tgz",
+      "integrity": "sha512-DEvV2ZF2r2/63V+tK8hQvrR2ZGn10srHbXviTlcv7Kpzw8jWiNTqbVgjO3IY8RxrrOUF8VPMQQFysYYYv0YZxw==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=6"
+      }
+    },
     "node_modules/proxy-from-env": {
       "version": "2.1.0",
       "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-2.1.0.tgz",
@@ -5205,6 +5240,16 @@
         "react-dom": ">=16.8"
       }
     },
+    "node_modules/react-simple-code-editor": {
+      "version": "0.14.1",
+      "resolved": "https://registry.npmjs.org/react-simple-code-editor/-/react-simple-code-editor-0.14.1.tgz",
+      "integrity": "sha512-BR5DtNRy+AswWJECyA17qhUDvrrCZ6zXOCfkQY5zSmb96BVUbpVAv03WpcjcwtCwiLbIANx3gebHOcXYn1EHow==",
+      "license": "MIT",
+      "peerDependencies": {
+        "react": ">=16.8.0",
+        "react-dom": ">=16.8.0"
+      }
+    },
     "node_modules/read-cache": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/read-cache/-/read-cache-1.0.0.tgz",
@@ -6310,6 +6355,33 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/xterm": {
+      "version": "5.3.0",
+      "resolved": "https://registry.npmjs.org/xterm/-/xterm-5.3.0.tgz",
+      "integrity": "sha512-8QqjlekLUFTrU6x7xck1MsPzPA571K5zNqWm0M0oroYEWVOptZ0+ubQSkQ3uxIEhcIHRujJy6emDWX4A7qyFzg==",
+      "deprecated": "This package is now deprecated. Move to @xterm/xterm instead.",
+      "license": "MIT"
+    },
+    "node_modules/xterm-addon-fit": {
+      "version": "0.8.0",
+      "resolved": "https://registry.npmjs.org/xterm-addon-fit/-/xterm-addon-fit-0.8.0.tgz",
+      "integrity": "sha512-yj3Np7XlvxxhYF/EJ7p3KHaMt6OdwQ+HDu573Vx1lRXsVxOcnVJs51RgjZOouIZOczTsskaS+CpXspK81/DLqw==",
+      "deprecated": "This package is now deprecated. Move to @xterm/addon-fit instead.",
+      "license": "MIT",
+      "peerDependencies": {
+        "xterm": "^5.0.0"
+      }
+    },
+    "node_modules/xterm-addon-web-links": {
+      "version": "0.9.0",
+      "resolved": "https://registry.npmjs.org/xterm-addon-web-links/-/xterm-addon-web-links-0.9.0.tgz",
+      "integrity": "sha512-LIzi4jBbPlrKMZF3ihoyqayWyTXAwGfu4yprz1aK2p71e9UKXN6RRzVONR0L+Zd+Ik5tPVI9bwp9e8fDTQh49Q==",
+      "deprecated": "This package is now deprecated. Move to @xterm/addon-web-links instead.",
+      "license": "MIT",
+      "peerDependencies": {
+        "xterm": "^5.0.0"
+      }
+    },
     "node_modules/yallist": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz",

apps/web/package.json

@@ -11,11 +11,18 @@
     "test": "vitest run"
   },
   "dependencies": {
+    "@phosphor-icons/react": "^2.1.10",
+    "@types/prismjs": "^1.26.6",
     "axios": "^1.6.0",
+    "prismjs": "^1.30.0",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "react-router-dom": "^6.20.0",
-    "tailwindcss": "^3.3.0"
+    "react-simple-code-editor": "^0.14.1",
+    "tailwindcss": "^3.3.0",
+    "xterm": "^5.3.0",
+    "xterm-addon-fit": "^0.8.0",
+    "xterm-addon-web-links": "^0.9.0"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^6.9.1",

apps/web/public/preview.html

@@ -0,0 +1,796 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Headquarter - UI Preview</title>
+    <link rel="preconnect" href="https://fonts.googleapis.com">
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+    <link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=IBM+Plex+Mono:wght@400;500&display=swap" rel="stylesheet">
+    <style>
+        :root {
+            --bg: #f4f1ea;
+            --panel: #fffef9;
+            --ink: #1d1d1b;
+            --muted: #5f5b55;
+            --brand: #275d4b;
+            --brand-strong: #154236;
+            --border: #d8d0c5;
+            --primary: #275d4b;
+            --primary-fg: #fffef9;
+            --color-primary: #275d4b;
+            --success: #2f8f62;
+            --success-light: rgba(47, 143, 98, 0.14);
+            --warning: #c08a1e;
+            --warning-light: rgba(192, 138, 30, 0.14);
+            --danger: #b94a3c;
+            --danger-light: rgba(185, 74, 60, 0.14);
+            --info: #4f7fb8;
+            --info-light: rgba(79, 127, 184, 0.14);
+            --space-1: 0.25rem;
+            --space-2: 0.5rem;
+            --space-3: 0.75rem;
+            --space-4: 1rem;
+            --space-5: 1.5rem;
+            --space-6: 2rem;
+            --font-size-xs: clamp(0.625rem, 0.6rem + 0.125vw, 0.75rem);
+            --font-size-sm: clamp(0.75rem, 0.7rem + 0.25vw, 0.875rem);
+            --font-size-base: clamp(0.875rem, 0.8rem + 0.35vw, 1rem);
+            --font-size-lg: clamp(1rem, 0.9rem + 0.5vw, 1.25rem);
+            --font-size-xl: clamp(1.25rem, 1.1rem + 0.75vw, 1.5rem);
+        }
+
+        * {
+            box-sizing: border-box;
+            margin: 0;
+            padding: 0;
+        }
+
+        body {
+            font-family: "Inter", "IBM Plex Sans", "Segoe UI", sans-serif;
+            background: var(--bg);
+            color: var(--ink);
+            line-height: 1.5;
+        }
+
+        /* App Shell */
+        .shell {
+            min-height: 100vh;
+            display: flex;
+            flex-direction: column;
+        }
+
+        .shell-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: center;
+            padding: 0.85rem 1.25rem;
+            border-bottom: 1px solid var(--border);
+            background: color-mix(in srgb, var(--panel) 88%, transparent);
+            backdrop-filter: blur(7px);
+        }
+
+        .brand {
+            font-weight: 700;
+            letter-spacing: 0.02em;
+            color: var(--ink);
+            text-decoration: none;
+        }
+
+        .header-actions {
+            display: flex;
+            align-items: center;
+            gap: 0.75rem;
+        }
+
+        .user-chip {
+            border: 1px solid var(--border);
+            background: var(--panel);
+            border-radius: 999px;
+            padding: 0.35rem 0.7rem;
+            font-size: 0.9rem;
+            color: var(--ink);
+            text-decoration: none;
+        }
+
+        .ghost-button {
+            border: 1px solid var(--border);
+            background: transparent;
+            border-radius: 10px;
+            padding: 0.58rem 0.85rem;
+            cursor: pointer;
+            font: inherit;
+            color: var(--muted);
+        }
+
+        .shell-body {
+            display: grid;
+            grid-template-columns: 230px 1fr;
+            min-height: calc(100vh - 57px);
+        }
+
+        .shell-nav {
+            border-right: 1px solid var(--border);
+            padding: 1rem 0.75rem;
+            display: flex;
+            flex-direction: column;
+            gap: 0.4rem;
+            background: color-mix(in srgb, var(--panel) 65%, transparent);
+        }
+
+        .nav-item {
+            padding: 0.65rem 0.75rem;
+            border-radius: 10px;
+            color: var(--muted);
+            text-decoration: none;
+            display: flex;
+            align-items: center;
+            gap: 0.5rem;
+            font-size: 0.95rem;
+        }
+
+        .nav-item:hover {
+            background: #ece7df;
+            color: var(--ink);
+        }
+
+        .nav-item-active {
+            background: var(--brand);
+            color: #f7fff7;
+        }
+
+        .nav-badge {
+            display: inline-flex;
+            align-items: center;
+            justify-content: center;
+            min-width: 18px;
+            height: 18px;
+            padding: 0 5px;
+            background: var(--primary);
+            color: var(--primary-fg);
+            border-radius: 9px;
+            font-size: 11px;
+            font-weight: 600;
+            margin-left: auto;
+        }
+
+        .nav-divider {
+            height: 1px;
+            background: var(--border);
+            margin: 0.5rem 0;
+        }
+
+        .nav-section-title {
+            margin-top: 0.5rem;
+            padding: 0.25rem 0.75rem;
+            font-size: var(--font-size-xs);
+            text-transform: uppercase;
+            letter-spacing: 0.08em;
+            color: var(--muted);
+        }
+
+        .session-item {
+            font-size: 0.85rem;
+            padding: 0.5rem 0.75rem;
+        }
+
+        .session-status {
+            width: 8px;
+            height: 8px;
+            border-radius: 50%;
+            background: var(--muted);
+            display: inline-block;
+            margin-right: 0.25rem;
+        }
+
+        .session-status.running {
+            background: var(--success);
+        }
+
+        .shell-content {
+            padding: 1.25rem;
+            overflow-x: hidden;
+        }
+
+        /* Common Components */
+        .stack {
+            display: flex;
+            flex-direction: column;
+            gap: 1rem;
+        }
+
+        .stack-sm {
+            gap: 0.5rem;
+        }
+
+        .card {
+            background: var(--panel);
+            border: 1px solid var(--border);
+            border-radius: 14px;
+            padding: 1rem;
+        }
+
+        .muted {
+            color: var(--muted);
+        }
+
+        .eyebrow {
+            margin: 0;
+            font-size: var(--font-size-xs);
+            text-transform: uppercase;
+            letter-spacing: 0.08em;
+            color: var(--muted);
+        }
+
+        .page-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: center;
+            flex-wrap: wrap;
+            gap: var(--space-3);
+        }
+
+        .primary-button {
+            background: var(--brand);
+            color: white;
+            border-radius: 10px;
+            border: 1px solid transparent;
+            padding: 0.58rem 0.85rem;
+            cursor: pointer;
+            font: inherit;
+        }
+
+        .primary-button:hover {
+            background: var(--brand-strong);
+        }
+
+        .secondary-button {
+            border-color: var(--border);
+            background: var(--panel);
+            border-radius: 10px;
+            border: 1px solid var(--border);
+            padding: 0.58rem 0.85rem;
+            cursor: pointer;
+            font: inherit;
+        }
+
+        /* Home Page */
+        .home-page {
+            max-width: 1240px;
+        }
+
+        .home-hero {
+            display: flex;
+            justify-content: space-between;
+            gap: var(--space-4);
+            align-items: flex-start;
+        }
+
+        .home-hero-actions {
+            display: flex;
+            gap: var(--space-2);
+            flex-wrap: wrap;
+        }
+
+        .home-summary-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(180px, 1fr));
+            gap: var(--space-4);
+        }
+
+        .home-summary-card .card-label {
+            margin: 0;
+            color: var(--muted);
+            font-size: 0.875rem;
+        }
+
+        .home-summary-card .card-value {
+            margin: 0.45rem 0 0;
+            font-size: 1.6rem;
+            font-weight: 700;
+        }
+
+        .home-section h2,
+        .home-section h3 {
+            margin: 0;
+        }
+
+        .home-session-grid,
+        .home-project-grid {
+            display: grid;
+            gap: var(--space-4);
+            grid-template-columns: repeat(auto-fit, minmax(280px, 1fr));
+        }
+
+        .session-card {
+            box-shadow: 0 1px 0 rgba(0, 0, 0, 0.02);
+        }
+
+        .session-actions {
+            display: flex;
+            gap: var(--space-2);
+            flex-wrap: wrap;
+        }
+
+        .status-badge {
+            display: inline-flex;
+            align-items: center;
+            padding: 2px 8px;
+            border-radius: 4px;
+            font-size: 12px;
+            font-weight: 500;
+            text-transform: capitalize;
+        }
+
+        .status-badge.running {
+            background: var(--success-light);
+            color: var(--success);
+        }
+
+        .status-badge.building {
+            background: var(--warning-light);
+            color: var(--warning);
+        }
+
+        .status-badge.pending {
+            background: var(--info-light);
+            color: var(--info);
+        }
+
+        .recent-sessions-list {
+            display: flex;
+            flex-direction: column;
+            gap: var(--space-2);
+        }
+
+        .recent-session-item {
+            display: flex;
+            justify-content: space-between;
+            align-items: center;
+            padding: var(--space-3) var(--space-4);
+            background: var(--bg);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+        }
+
+        .recent-session-name {
+            font-weight: 500;
+        }
+
+        .create-session-form .form-row {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
+            gap: var(--space-4);
+        }
+
+        .form-field {
+            display: flex;
+            flex-direction: column;
+            gap: 0.35rem;
+        }
+
+        .form-field input,
+        .form-field select,
+        .form-field textarea {
+            padding: 0.55rem 0.7rem;
+            border: 1px solid var(--border);
+            border-radius: 10px;
+            font: inherit;
+            background: var(--panel);
+            color: var(--ink);
+        }
+
+        .form-actions {
+            display: flex;
+            gap: var(--space-3);
+            align-items: center;
+            flex-wrap: wrap;
+        }
+
+        /* Settings Page */
+        .settings-page {
+            max-width: 1240px;
+        }
+
+        .settings-header {
+            padding: 1.5rem;
+        }
+
+        .settings-tabs {
+            display: flex;
+            gap: var(--space-2);
+            flex-wrap: wrap;
+        }
+
+        .settings-tab {
+            padding: 0.6rem 0.9rem;
+            border-radius: 999px;
+            border: 1px solid var(--border);
+            color: var(--muted);
+            background: var(--panel);
+            text-decoration: none;
+            cursor: pointer;
+        }
+
+        .settings-tab.active {
+            background: var(--brand);
+            color: white;
+            border-color: transparent;
+        }
+
+        .settings-panel {
+            padding: 1.5rem;
+        }
+
+        .settings-actions {
+            display: flex;
+            gap: var(--space-3);
+            align-items: center;
+            flex-wrap: wrap;
+        }
+
+        .success-text {
+            color: var(--success);
+        }
+
+        .error-text {
+            color: var(--danger);
+        }
+
+        /* Preview Switcher */
+        .preview-switcher {
+            position: fixed;
+            bottom: 1rem;
+            right: 1rem;
+            display: flex;
+            gap: 0.5rem;
+            background: var(--panel);
+            border: 1px solid var(--border);
+            border-radius: 10px;
+            padding: 0.5rem;
+            box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1);
+            z-index: 1000;
+        }
+
+        .preview-switcher button {
+            padding: 0.5rem 1rem;
+            border: none;
+            background: transparent;
+            border-radius: 6px;
+            cursor: pointer;
+            font: inherit;
+            color: var(--muted);
+        }
+
+        .preview-switcher button.active {
+            background: var(--brand);
+            color: white;
+        }
+
+        .page-preview {
+            display: none;
+        }
+
+        .page-preview.active {
+            display: block;
+        }
+
+        /* Responsive */
+        @media (max-width: 767px) {
+            .shell-body {
+                grid-template-columns: 1fr;
+            }
+            .shell-nav {
+                flex-direction: row;
+                overflow-x: auto;
+                border-right: none;
+                border-bottom: 1px solid var(--border);
+            }
+            .home-hero {
+                flex-direction: column;
+            }
+        }
+    </style>
+</head>
+<body>
+    <div class="shell">
+        <header class="shell-header">
+            <a href="#" class="brand">Headquarter</a>
+            <div class="header-actions">
+                <a href="#" class="user-chip">User</a>
+                <button class="ghost-button">Logout</button>
+            </div>
+        </header>
+
+        <div class="shell-body">
+            <aside class="shell-nav" aria-label="Primary navigation">
+                <a href="#" class="nav-item nav-item-active">
+                    <span>🏠</span> Home
+                    <span class="nav-badge">3</span>
+                </a>
+                <a href="#" class="nav-item">
+                    <span>📁</span> Projects
+                </a>
+                <a href="#" class="nav-item">
+                    <span>⚙️</span> Settings
+                </a>
+
+                <div class="nav-divider"></div>
+                <div class="nav-section-title">Live sessions</div>
+                <a href="#" class="nav-item session-item">
+                    <span class="session-status running"></span>
+                    <span>Dev Environment</span>
+                </a>
+                <a href="#" class="nav-item session-item">
+                    <span class="session-status running"></span>
+                    <span>Jupyter Lab</span>
+                </a>
+                <a href="#" class="nav-item session-item">
+                    <span class="session-status"></span>
+                    <span>Code Server</span>
+                </a>
+            </aside>
+
+            <main class="shell-content">
+                <!-- HOME PAGE PREVIEW -->
+                <div id="home-preview" class="page-preview active">
+                    <section class="stack home-page">
+                        <header class="home-hero card">
+                            <div class="stack-sm">
+                                <p class="eyebrow">Workspace overview</p>
+                                <h1>Home</h1>
+                                <p class="muted">Open sessions, available projects, and the fastest path back into work.</p>
+                            </div>
+                            <div class="home-hero-actions">
+                                <button class="primary-button">New Project</button>
+                                <button class="secondary-button">Settings</button>
+                            </div>
+                        </header>
+
+                        <div class="home-summary-grid">
+                            <article class="card home-summary-card">
+                                <p class="card-label">Open sessions</p>
+                                <p class="card-value">3</p>
+                            </article>
+                            <article class="card home-summary-card">
+                                <p class="card-label">Projects</p>
+                                <p class="card-value">5</p>
+                            </article>
+                            <article class="card home-summary-card">
+                                <p class="card-label">Repositories</p>
+                                <p class="card-value">12</p>
+                            </article>
+                        </div>
+
+                        <section class="card stack home-section">
+                            <div class="page-header">
+                                <div>
+                                    <p class="eyebrow">Open sessions</p>
+                                    <h2>3</h2>
+                                </div>
+                            </div>
+                            <div class="home-session-grid">
+                                <article class="card session-card">
+                                    <div class="stack-sm">
+                                        <div style="display: flex; gap: 0.5rem; align-items: center;">
+                                            <h3>Dev Environment</h3>
+                                            <span class="status-badge running">running</span>
+                                        </div>
+                                        <p class="muted">Acme Corp · main</p>
+                                        <p class="muted">VS Code Server</p>
+                                    </div>
+                                    <div class="session-actions">
+                                        <button class="secondary-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Open</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Tunnel</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Stop</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem; color: var(--danger);">Delete</button>
+                                    </div>
+                                </article>
+
+                                <article class="card session-card">
+                                    <div class="stack-sm">
+                                        <div style="display: flex; gap: 0.5rem; align-items: center;">
+                                            <h3>Jupyter Lab</h3>
+                                            <span class="status-badge running">running</span>
+                                        </div>
+                                        <p class="muted">Data Science · experiments</p>
+                                        <p class="muted">Jupyter Notebook</p>
+                                    </div>
+                                    <div class="session-actions">
+                                        <button class="secondary-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Open</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Tunnel</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Stop</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem; color: var(--danger);">Delete</button>
+                                    </div>
+                                </article>
+
+                                <article class="card session-card">
+                                    <div class="stack-sm">
+                                        <div style="display: flex; gap: 0.5rem; align-items: center;">
+                                            <h3>Database Console</h3>
+                                            <span class="status-badge building">building</span>
+                                        </div>
+                                        <p class="muted">Backend API · staging</p>
+                                        <p class="muted">PostgreSQL Client</p>
+                                    </div>
+                                    <div class="session-actions">
+                                        <button class="secondary-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Open</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Tunnel</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Stop</button>
+                                        <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem; color: var(--danger);">Delete</button>
+                                    </div>
+                                </article>
+                            </div>
+                        </section>
+
+                        <section class="card stack home-section">
+                            <div class="page-header">
+                                <div>
+                                    <p class="eyebrow">Available projects</p>
+                                    <h2>5</h2>
+                                </div>
+                                <button class="secondary-button">View all</button>
+                            </div>
+                            <div class="home-project-grid">
+                                <article class="card" style="box-shadow: 0 1px 0 rgba(0,0,0,0.02);">
+                                    <div class="stack-sm">
+                                        <h3>Acme Corp</h3>
+                                        <p class="muted">Main product development</p>
+                                    </div>
+                                    <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem; margin-top: 0.5rem;">Open Workspace</button>
+                                </article>
+
+                                <article class="card" style="box-shadow: 0 1px 0 rgba(0,0,0,0.02);">
+                                    <div class="stack-sm">
+                                        <h3>Data Science</h3>
+                                        <p class="muted">ML experiments and notebooks</p>
+                                    </div>
+                                    <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem; margin-top: 0.5rem;">Open Workspace</button>
+                                </article>
+
+                                <article class="card" style="box-shadow: 0 1px 0 rgba(0,0,0,0.02);">
+                                    <div class="stack-sm">
+                                        <h3>Backend API</h3>
+                                        <p class="muted">REST API services</p>
+                                    </div>
+                                    <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem; margin-top: 0.5rem;">Open Workspace</button>
+                                </article>
+                            </div>
+                        </section>
+
+                        <section class="card stack home-section">
+                            <div class="page-header">
+                                <div>
+                                    <p class="eyebrow">Quick create</p>
+                                    <h2>Start a session</h2>
+                                </div>
+                            </div>
+                            <form class="stack create-session-form">
+                                <div class="form-row">
+                                    <label class="form-field">
+                                        Project
+                                        <select>
+                                            <option>Select project...</option>
+                                            <option>Acme Corp</option>
+                                            <option>Data Science</option>
+                                        </select>
+                                    </label>
+                                    <label class="form-field">
+                                        Repository
+                                        <select disabled>
+                                            <option>Select repository...</option>
+                                        </select>
+                                    </label>
+                                    <label class="form-field">
+                                        Tool type
+                                        <select>
+                                            <option>Select tool...</option>
+                                            <option>VS Code Server</option>
+                                            <option>Jupyter Lab</option>
+                                        </select>
+                                    </label>
+                                </div>
+                                <label class="form-field">
+                                    Display name
+                                    <input type="text" placeholder="My Development Environment">
+                                </label>
+                                <div class="form-actions">
+                                    <button class="primary-button" type="submit">Create Session</button>
+                                </div>
+                            </form>
+                        </section>
+
+                        <section class="card stack home-section">
+                            <div class="page-header">
+                                <div>
+                                    <p class="eyebrow">Recent sessions</p>
+                                    <h2>2</h2>
+                                </div>
+                            </div>
+                            <div class="recent-sessions-list">
+                                <article class="recent-session-item">
+                                    <div style="display: flex; flex-direction: column; gap: 0.25rem;">
+                                        <span class="recent-session-name">Old Dev Box</span>
+                                        <span class="muted">Acme Corp · VS Code Server</span>
+                                    </div>
+                                    <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Open</button>
+                                </article>
+                                <article class="recent-session-item">
+                                    <div style="display: flex; flex-direction: column; gap: 0.25rem;">
+                                        <span class="recent-session-name">ML Training</span>
+                                        <span class="muted">Data Science · Jupyter Lab</span>
+                                    </div>
+                                    <button class="ghost-button" style="font-size: 0.85rem; padding: 0.42rem 0.7rem;">Open</button>
+                                </article>
+                            </div>
+                        </section>
+                    </section>
+                </div>
+
+                <!-- SETTINGS PAGE PREVIEW -->
+                <div id="settings-preview" class="page-preview">
+                    <section class="stack settings-page">
+                        <header class="settings-header card stack-sm">
+                            <div>
+                                <p class="eyebrow">Configuration</p>
+                                <h1>Settings</h1>
+                            </div>
+                            <p class="muted">General preferences, SSH keys, tool types, and tool configs live here.</p>
+                        </header>
+
+                        <nav class="settings-tabs" aria-label="Settings sections">
+                            <a href="#" class="settings-tab active">General</a>
+                            <a href="#" class="settings-tab">SSH Keys</a>
+                            <a href="#" class="settings-tab">Tool Types</a>
+                            <a href="#" class="settings-tab">Tool Configs</a>
+                        </nav>
+
+                        <div class="settings-panel card">
+                            <div class="stack">
+                                <h2>General</h2>
+                                <label class="form-field">
+                                    Theme
+                                    <select>
+                                        <option>System</option>
+                                        <option>Light</option>
+                                        <option>Dark</option>
+                                    </select>
+                                </label>
+                                <label class="form-field">
+                                    Git user name
+                                    <input type="text" placeholder="Your git commit name" value="John Doe">
+                                </label>
+                                <label class="form-field">
+                                    Git user email
+                                    <input type="email" placeholder="your.email@example.com" value="john@example.com">
+                                </label>
+                                <label class="form-field">
+                                    Default editor
+                                    <input type="text" placeholder="e.g., vscode, vim, cursor" value="vscode">
+                                </label>
+                                <div class="settings-actions">
+                                    <button class="primary-button">Save Settings</button>
+                                </div>
+                            </div>
+                        </div>
+                    </section>
+                </div>
+            </main>
+        </div>
+    </div>
+
+    <div class="preview-switcher">
+        <button class="active" onclick="showPage('home')">Home</button>
+        <button onclick="showPage('settings')">Settings</button>
+    </div>
+
+    <script>
+        function showPage(page) {
+            document.querySelectorAll('.page-preview').forEach(p => p.classList.remove('active'));
+            document.querySelectorAll('.preview-switcher button').forEach(b => b.classList.remove('active'));
+            document.getElementById(page + '-preview').classList.add('active');
+            event.target.classList.add('active');
+        }
+    </script>
+</body>
+</html>

apps/web/src/api/config_folders.test.ts

@@ -0,0 +1,131 @@
+import { describe, expect, it, vi } from "vitest";
+
+import {
+  createConfigFolder,
+  deleteConfigFolder,
+  listConfigFolders,
+  updateConfigFolder,
+} from "../api/config_folders";
+
+const mockGet = vi.fn();
+const mockPost = vi.fn();
+const mockPut = vi.fn();
+const mockDelete = vi.fn();
+
+vi.mock("../api/client", () => ({
+  apiClient: {
+    get: (...args: unknown[]) => mockGet(...args),
+    post: (...args: unknown[]) => mockPost(...args),
+    put: (...args: unknown[]) => mockPut(...args),
+    delete: (...args: unknown[]) => mockDelete(...args),
+    interceptors: {
+      response: {
+        use: vi.fn(),
+      },
+    },
+  },
+  shouldSkipAuthRedirect: vi.fn(() => false),
+}));
+
+describe("config_folders API", () => {
+  describe("listConfigFolders", () => {
+    it("returns folders with files and overrides", async () => {
+      const mockResponse = {
+        data: [
+          {
+            id: "folder-1",
+            name: "my-dotfiles",
+            description: "My personal config files",
+            mount_path: "/home/user",
+            files: { ".zshrc": "export ZSH=\"$HOME/.oh-my-zsh\"" },
+            project_overrides: {},
+            is_active: true,
+            user_id: "user-1",
+            created_at: "2024-01-01T00:00:00Z",
+            updated_at: "2024-01-01T00:00:00Z",
+          },
+        ],
+      };
+      mockGet.mockResolvedValue(mockResponse);
+
+      const result = await listConfigFolders();
+
+      expect(result[0].name).toBe("my-dotfiles");
+      expect(result[0].files).toEqual({ ".zshrc": "export ZSH=\"$HOME/.oh-my-zsh\"" });
+      expect(mockGet).toHaveBeenCalledWith("/config-folders");
+    });
+  });
+
+  describe("createConfigFolder", () => {
+    it("creates folder with files", async () => {
+      const mockResponse = {
+        data: {
+          id: "folder-new",
+          name: "new-folder",
+          mount_path: "/workspace",
+          files: { ".env": "API_URL=http://localhost" },
+          is_active: true,
+          user_id: "user-1",
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      };
+      mockPost.mockResolvedValue(mockResponse);
+
+      const result = await createConfigFolder({
+        name: "new-folder",
+        mount_path: "/workspace",
+        files: { ".env": "API_URL=http://localhost" },
+      });
+
+      expect(result.name).toBe("new-folder");
+      expect(mockPost).toHaveBeenCalledWith(
+        "/config-folders",
+        expect.objectContaining({
+          name: "new-folder",
+          mount_path: "/workspace",
+        })
+      );
+    });
+  });
+
+  describe("updateConfigFolder", () => {
+    it("updates folder files", async () => {
+      const mockResponse = {
+        data: {
+          id: "folder-1",
+          name: "updated-folder",
+          mount_path: "/home/user",
+          files: { ".bashrc": "alias ll='ls -la'" },
+          is_active: true,
+          user_id: "user-1",
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      };
+      mockPut.mockResolvedValue(mockResponse);
+
+      const result = await updateConfigFolder("folder-1", {
+        files: { ".bashrc": "alias ll='ls -la'" },
+      });
+
+      expect(result.files).toEqual({ ".bashrc": "alias ll='ls -la'" });
+      expect(mockPut).toHaveBeenCalledWith(
+        "/config-folders/folder-1",
+        expect.objectContaining({
+          files: { ".bashrc": "alias ll='ls -la'" },
+        })
+      );
+    });
+  });
+
+  describe("deleteConfigFolder", () => {
+    it("deletes folder", async () => {
+      mockDelete.mockResolvedValue({ data: undefined });
+
+      await deleteConfigFolder("folder-1");
+
+      expect(mockDelete).toHaveBeenCalledWith("/config-folders/folder-1");
+    });
+  });
+});

apps/web/src/api/config_folders.ts

@@ -0,0 +1,95 @@
+import { apiClient } from "./client";
+
+export interface ConfigFolder {
+  id: string;
+  user_id: string;
+  name: string;
+  description: string | null;
+  mount_path: string;
+  files: Record<string, string>;
+  project_overrides: Record<string, { mount_path?: string; files?: Record<string, string> }> | null;
+  is_active: boolean;
+  created_at: string;
+  updated_at: string;
+}
+
+export interface CreateConfigFolderRequest {
+  name: string;
+  description?: string;
+  mount_path: string;
+  files?: Record<string, string>;
+  is_active?: boolean;
+}
+
+export interface UpdateConfigFolderRequest {
+  name?: string;
+  description?: string;
+  mount_path?: string;
+  files?: Record<string, string>;
+  is_active?: boolean;
+}
+
+export interface ProjectOverrideRequest {
+  mount_path?: string;
+  files?: Record<string, string>;
+}
+
+export const listConfigFolders = async (): Promise<ConfigFolder[]> => {
+  const response = await apiClient.get<ConfigFolder[]>("/config-folders");
+  return response.data;
+};
+
+export const getConfigFolder = async (id: string): Promise<ConfigFolder> => {
+  const response = await apiClient.get<ConfigFolder>(`/config-folders/${id}`);
+  return response.data;
+};
+
+export const createConfigFolder = async (
+  data: CreateConfigFolderRequest
+): Promise<ConfigFolder> => {
+  const response = await apiClient.post<ConfigFolder>("/config-folders", data);
+  return response.data;
+};
+
+export const updateConfigFolder = async (
+  id: string,
+  data: UpdateConfigFolderRequest
+): Promise<ConfigFolder> => {
+  const response = await apiClient.put<ConfigFolder>(`/config-folders/${id}`, data);
+  return response.data;
+};
+
+export const deleteConfigFolder = async (id: string): Promise<void> => {
+  await apiClient.delete(`/config-folders/${id}`);
+};
+
+export const addProjectOverride = async (
+  id: string,
+  projectId: string,
+  data: ProjectOverrideRequest
+): Promise<ConfigFolder> => {
+  const response = await apiClient.post<ConfigFolder>(
+    `/config-folders/${id}/overrides/${projectId}`,
+    data
+  );
+  return response.data;
+};
+
+export const updateProjectOverride = async (
+  id: string,
+  projectId: string,
+  data: ProjectOverrideRequest
+): Promise<ConfigFolder> => {
+  const response = await apiClient.put<ConfigFolder>(
+    `/config-folders/${id}/overrides/${projectId}`,
+    data
+  );
+  return response.data;
+};
+
+export const deleteProjectOverride = async (
+  id: string,
+  projectId: string
+): Promise<void> => {
+  await apiClient.delete(`/config-folders/${id}/overrides/${projectId}`);
+};

apps/web/src/api/git_repositories.ts

@@ -15,6 +15,22 @@ export interface GitRepository {
 export interface GitRepositoryCreate {
   name: string;
   remote_url?: string;
+  force_original_url?: boolean;
+}
+
+export interface URLParseResult {
+  original_url: string;
+  base_url: string | null;
+  is_valid_clone_url: boolean;
+  needs_parsing: boolean;
+  host: string | null;
+  message: string;
+  error_code: string | null;
+}
+
+export async function parseGitUrl(url: string): Promise<URLParseResult> {
+  const response = await apiClient.post("/projects/repositories/parse-url", { url });
+  return response.data;
 }
 
 export async function listRepositories(projectId: string): Promise<GitRepository[]> {
@@ -33,3 +49,197 @@ export async function createRepository(
 export async function deleteRepository(projectId: string, repoId: string): Promise<void> {
   await apiClient.delete(`/projects/${projectId}/repositories/${repoId}`);
 }
+
+export interface CommitHistoryEntry {
+  hash: string;
+  short_hash: string;
+  message: string;
+  author_name: string;
+  author_email: string;
+  author_date: string;
+  refs: string[];
+  graph_symbol: string;
+  graph_depth: number;
+}
+
+export interface CommitHistoryResponse {
+  commits: CommitHistoryEntry[];
+  branches: string[];
+  tags: string[];
+}
+
+export async function getRepositoryHistory(
+  projectId: string,
+  repoId: string,
+  branch?: string,
+  limit?: number
+): Promise<CommitHistoryResponse> {
+  const searchParams = new URLSearchParams();
+  if (branch) searchParams.set("branch", branch);
+  if (limit) searchParams.set("limit", String(limit));
+  const queryString = searchParams.toString();
+  const params = queryString ? `?${queryString}` : "";
+  const response = await apiClient.get(`/projects/${projectId}/repositories/${repoId}/history${params}`);
+  return response.data;
+}
+
+export interface CommitDetail {
+  hash: string;
+  short_hash: string;
+  message: string;
+  author_name: string;
+  author_email: string;
+  author_date: string;
+  committer_name: string;
+  committer_email: string;
+  committer_date: string;
+  stats: {
+    additions: number;
+    deletions: number;
+    files_changed: number;
+  };
+  diff: string;
+  parents: string[];
+}
+
+export async function getCommitDetail(
+  projectId: string,
+  repoId: string,
+  commitHash: string
+): Promise<CommitDetail> {
+  const response = await apiClient.get(
+    `/projects/${projectId}/repositories/${repoId}/commits/${commitHash}`
+  );
+  return response.data;
+}
+
+// Git Control API
+
+export interface GitStatus {
+  branch: string;
+  modified: string[];
+  added: string[];
+  deleted: string[];
+  untracked: string[];
+  renamed: string[];
+  ahead: number;
+  behind: number;
+}
+
+export async function getRepositoryStatus(
+  projectId: string,
+  repoId: string
+): Promise<GitStatus> {
+  const response = await apiClient.get(
+    `/projects/${projectId}/repositories/${repoId}/status`
+  );
+  return response.data;
+}
+
+export async function createBranch(
+  projectId: string,
+  repoId: string,
+  name: string,
+  baseBranch: string = "HEAD"
+): Promise<{ message: string; branch: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/branches`,
+    { name, base_branch: baseBranch }
+  );
+  return response.data;
+}
+
+export async function deleteBranch(
+  projectId: string,
+  repoId: string,
+  branchName: string,
+  force: boolean = false
+): Promise<{ message: string }> {
+  const response = await apiClient.delete(
+    `/projects/${projectId}/repositories/${repoId}/branches/${branchName}?force=${force}`
+  );
+  return response.data;
+}
+
+export async function checkoutBranch(
+  projectId: string,
+  repoId: string,
+  branch: string
+): Promise<{ message: string; branch: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/checkout`,
+    { branch }
+  );
+  return response.data;
+}
+
+export interface CommitResponse {
+  commit_hash: string;
+  message: string;
+}
+
+export async function commitChanges(
+  projectId: string,
+  repoId: string,
+  message: string,
+  files?: string[]
+): Promise<CommitResponse> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/commit`,
+    { message, files }
+  );
+  return response.data;
+}
+
+export async function fetchRepository(
+  projectId: string,
+  repoId: string
+): Promise<{ message: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/fetch`
+  );
+  return response.data;
+}
+
+export async function pullRepository(
+  projectId: string,
+  repoId: string,
+  branch?: string
+): Promise<{ message: string }> {
+  const params = branch ? `?branch=${branch}` : "";
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/pull${params}`
+  );
+  return response.data;
+}
+
+export async function pushRepository(
+  projectId: string,
+  repoId: string,
+  branch?: string
+): Promise<{ message: string }> {
+  const params = branch ? `?branch=${branch}` : "";
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/push${params}`
+  );
+  return response.data;
+}
+
+export interface MergeResponse {
+  commit_hash: string;
+  message: string;
+}
+
+export async function mergeBranches(
+  projectId: string,
+  repoId: string,
+  sourceBranch: string,
+  targetBranch?: string,
+  message?: string
+): Promise<MergeResponse> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/merge`,
+    { source_branch: sourceBranch, target_branch: targetBranch, message }
+  );
+  return response.data;
+}

apps/web/src/api/sessions.ts

@@ -0,0 +1,124 @@
+import { apiClient } from "./client";
+
+export interface ToolInstance {
+  id: string;
+  name: string;
+  display_name: string;
+  tool_type_id: string;
+  tool_type_name: string;
+  tool_type_interfaces: string[];
+  status: string;
+  url: string | null;
+  port: number | null;
+  created_at: string;
+}
+
+export interface Session {
+  id: string;
+  display_name: string;
+  tool_type_name: string;
+  tool_icon: string;
+  tool_type_interfaces: string[];
+  repository_name: string;
+  repository_id: string;
+  project_name: string;
+  project_id: string;
+  status: string;
+  url: string | null;
+}
+
+export async function listInstances(
+  projectId: string,
+  repoId: string
+): Promise<ToolInstance[]> {
+  const response = await apiClient.get(
+    `/projects/${projectId}/repositories/${repoId}/instances`
+  );
+  return response.data.instances;
+}
+
+export async function createInstance(
+  projectId: string,
+  repoId: string,
+  toolTypeId: string,
+  displayName?: string
+): Promise<ToolInstance> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/instances`,
+    {
+      tool_type_id: toolTypeId,
+      display_name: displayName,
+    }
+  );
+  return response.data;
+}
+
+export async function startInstance(
+  projectId: string,
+  repoId: string,
+  instanceId: string
+): Promise<{ status: string; url?: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/start`
+  );
+  return response.data;
+}
+
+export async function stopInstance(
+  projectId: string,
+  repoId: string,
+  instanceId: string
+): Promise<{ status: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/stop`
+  );
+  return response.data;
+}
+
+export async function restartInstance(
+  projectId: string,
+  repoId: string,
+  instanceId: string
+): Promise<{ status: string; url?: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/restart`
+  );
+  return response.data;
+}
+
+export async function deleteInstance(
+  projectId: string,
+  repoId: string,
+  instanceId: string
+): Promise<void> {
+  await apiClient.delete(
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}`
+  );
+}
+
+export async function getUserSessions(): Promise<Session[]> {
+  const response = await apiClient.get("/users/me/sessions");
+  return response.data.sessions;
+}
+
+export async function checkInstanceHealth(
+  projectId: string,
+  repoId: string,
+  instanceId: string
+): Promise<{ healthy: boolean; status_code: number | null; error?: string }> {
+  const response = await apiClient.get(
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/health`
+  );
+  return response.data;
+}
+
+export async function recreateInstanceTunnel(
+  projectId: string,
+  repoId: string,
+  instanceId: string
+): Promise<{ status: string; url?: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/recreate-tunnel`
+  );
+  return response.data;
+}

apps/web/src/api/settings.ts

@@ -5,13 +5,15 @@ export interface UserConfig {
   theme: string;
   git_user_name: string | null;
   git_user_email: string | null;
+  last_session_id: string | null;
 }
 
 export interface UserConfigUpdate {
-  default_editor?: string;
-  theme?: string;
-  git_user_name?: string;
-  git_user_email?: string;
+  default_editor?: string | null;
+  theme?: string | null;
+  git_user_name?: string | null;
+  git_user_email?: string | null;
+  last_session_id?: string | null;
 }
 
 export const getUserConfig = async (): Promise<UserConfig> => {

apps/web/src/api/tool_configs.ts

@@ -0,0 +1,75 @@
+import { apiClient } from "./client";
+
+export interface ToolConfig {
+  id: string;
+  tool_type_id: string;
+  project_id: string | null;
+  key: string;
+  value: string;
+  config_type: string;
+  file_path: string | null;
+  port_override: number | null;
+  start_command: string | null;
+  working_directory: string | null;
+  environment_variables: Record<string, string> | null;
+  volumes: Array<{ source: string; target: string; type?: string }> | null;
+}
+
+export interface CreateToolConfigRequest {
+  tool_type_id: string;
+  project_id?: string;
+  key: string;
+  value: string;
+  config_type?: string;
+  file_path?: string;
+  port_override?: number;
+  start_command?: string;
+  working_directory?: string;
+  environment_variables?: Record<string, string>;
+  volumes?: Array<{ source: string; target: string; type?: string }>;
+}
+
+export const listToolConfigs = async (
+  tool_type_id?: string,
+  project_id?: string
+): Promise<ToolConfig[]> => {
+  const params = new URLSearchParams();
+  if (tool_type_id) params.append("tool_type_id", tool_type_id);
+  if (project_id) params.append("project_id", project_id);
+  
+  const response = await apiClient.get<{ configs: ToolConfig[] }>(
+    `/tool-configs?${params.toString()}`
+  );
+  return response.data.configs;
+};
+
+export const createToolConfig = async (
+  data: CreateToolConfigRequest
+): Promise<ToolConfig> => {
+  const response = await apiClient.post<{ configs: ToolConfig[] }>("/tool-configs", data);
+  return response.data.configs[0];
+};
+
+export const updateToolConfig = async (
+  id: string,
+  data: CreateToolConfigRequest
+): Promise<ToolConfig> => {
+  const response = await apiClient.put<{ configs: ToolConfig[] }>(
+    `/tool-configs/${id}`,
+    data
+  );
+  return response.data.configs[0];
+};
+
+export const deleteToolConfig = async (id: string): Promise<void> => {
+  await apiClient.delete(`/tool-configs/${id}`);
+};
+
+export const getToolConfigDefaults = async (
+  toolTypeId: string
+): Promise<ToolConfig> => {
+  const response = await apiClient.get<ToolConfig>(
+    `/tool-configs/defaults/${toolTypeId}`
+  );
+  return response.data;
+};

apps/web/src/api/tool_types.test.ts

@@ -0,0 +1,227 @@
+import { describe, expect, it, vi } from "vitest";
+
+import {
+  createToolType,
+  deleteToolType,
+  listToolTypes,
+  updateToolType,
+  validateToolType,
+} from "../api/tool_types";
+
+const mockGet = vi.fn();
+const mockPost = vi.fn();
+const mockPut = vi.fn();
+const mockDelete = vi.fn();
+
+vi.mock("../api/client", () => ({
+  apiClient: {
+    get: (...args: unknown[]) => mockGet(...args),
+    post: (...args: unknown[]) => mockPost(...args),
+    put: (...args: unknown[]) => mockPut(...args),
+    delete: (...args: unknown[]) => mockDelete(...args),
+    interceptors: {
+      response: {
+        use: vi.fn(),
+      },
+    },
+  },
+  shouldSkipAuthRedirect: vi.fn(() => false),
+}));
+
+describe("tool_types API", () => {
+  describe("listToolTypes", () => {
+    it("returns tool types with new fields", async () => {
+      const mockResponse = {
+        data: [
+          {
+            id: "type-1",
+            name: "custom-tool",
+            display_name: "Custom Tool",
+            definition_type: "dockerfile",
+            dockerfile_template: "FROM python:3.11",
+            readiness_probe: {
+              command: "python --version",
+              timeout: 30,
+              interval: 2,
+            },
+            build_context: null,
+            created_at: "2024-01-01T00:00:00Z",
+            updated_at: "2024-01-01T00:00:00Z",
+          },
+        ],
+      };
+      mockGet.mockResolvedValue(mockResponse);
+
+      const result = await listToolTypes();
+
+      expect(result[0].definition_type).toBe("dockerfile");
+      expect(result[0].dockerfile_template).toBe("FROM python:3.11");
+      expect(result[0].readiness_probe).toEqual({
+        command: "python --version",
+        timeout: 30,
+        interval: 2,
+      });
+    });
+
+    it("returns compose tool types", async () => {
+      const mockResponse = {
+        data: [
+          {
+            id: "type-1",
+            name: "code-server",
+            definition_type: "compose",
+            compose_template: "version: '3.8'",
+            dockerfile_template: null,
+            build_context: null,
+            created_at: "2024-01-01T00:00:00Z",
+            updated_at: "2024-01-01T00:00:00Z",
+          },
+        ],
+      };
+      mockGet.mockResolvedValue(mockResponse);
+
+      const result = await listToolTypes();
+
+      expect(result[0].definition_type).toBe("compose");
+      expect(result[0].dockerfile_template).toBeNull();
+    });
+  });
+
+  describe("createToolType", () => {
+    it("creates tool type with dockerfile", async () => {
+      const mockResponse = {
+        data: {
+          id: "new-type",
+          name: "docker-tool",
+          definition_type: "dockerfile",
+          dockerfile_template: "FROM node:18",
+          build_context: null,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      };
+      mockPost.mockResolvedValue(mockResponse);
+
+      const result = await createToolType({
+        name: "docker-tool",
+        display_name: "Docker Tool",
+        definition_type: "dockerfile",
+        dockerfile_template: "FROM node:18",
+        default_port: 3000,
+        required_variables: [],
+      });
+
+      expect(result.definition_type).toBe("dockerfile");
+      expect(mockPost).toHaveBeenCalledWith(
+        "/tool-types",
+        expect.objectContaining({
+          definition_type: "dockerfile",
+          dockerfile_template: "FROM node:18",
+        })
+      );
+    });
+
+    it("creates tool type with readiness probe", async () => {
+      const mockResponse = {
+        data: {
+          id: "new-type",
+          name: "probed-tool",
+          readiness_probe: {
+            command: "curl -f http://localhost:8080",
+            timeout: 60,
+            interval: 3,
+          },
+          build_context: null,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      };
+      mockPost.mockResolvedValue(mockResponse);
+
+      const result = await createToolType({
+        name: "probed-tool",
+        display_name: "Probed Tool",
+        compose_template: "version: '3.8'",
+        default_port: 8080,
+        required_variables: [],
+        readiness_probe: {
+          command: "curl -f http://localhost:8080",
+          timeout: 60,
+          interval: 3,
+        },
+      });
+
+      expect(result.readiness_probe).toEqual({
+        command: "curl -f http://localhost:8080",
+        timeout: 60,
+        interval: 3,
+      });
+    });
+  });
+
+  describe("validateToolType", () => {
+    it("validates tool type by id", async () => {
+      const mockResponse = {
+        data: { valid: true, errors: [] },
+      };
+      mockGet.mockResolvedValue(mockResponse);
+
+      const result = await validateToolType("type-1");
+
+      expect(result.valid).toBe(true);
+      expect(mockGet).toHaveBeenCalledWith("/tool-types/type-1/validate");
+    });
+
+    it("returns validation errors", async () => {
+      const mockResponse = {
+        data: { valid: false, errors: ["Invalid YAML"] },
+      };
+      mockGet.mockResolvedValue(mockResponse);
+
+      const result = await validateToolType("type-1");
+
+      expect(result.valid).toBe(false);
+      expect(result.errors).toContain("Invalid YAML");
+    });
+  });
+
+  describe("updateToolType", () => {
+    it("updates tool type with new fields", async () => {
+      const mockResponse = {
+        data: {
+          id: "type-1",
+          name: "updated-tool",
+          definition_type: "dockerfile",
+          dockerfile_template: "FROM python:3.11",
+          build_context: null,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      };
+      mockPut.mockResolvedValue(mockResponse);
+
+      const result = await updateToolType("type-1", {
+        definition_type: "dockerfile",
+        dockerfile_template: "FROM python:3.11",
+      });
+
+      expect(result.definition_type).toBe("dockerfile");
+      expect(mockPut).toHaveBeenCalledWith(
+        "/tool-types/type-1",
+        expect.objectContaining({
+          definition_type: "dockerfile",
+        })
+      );
+    });
+  });
+
+  describe("deleteToolType", () => {
+    it("deletes tool type", async () => {
+      mockDelete.mockResolvedValue({ data: undefined });
+
+      await deleteToolType("type-1");
+
+      expect(mockDelete).toHaveBeenCalledWith("/tool-types/type-1");
+    });
+  });
+});

apps/web/src/api/tool_types.ts

@@ -1,11 +1,24 @@
 import { apiClient } from "./client";
 
+export interface ReadinessProbe {
+  command: string;
+  timeout: number;
+  interval: number;
+}
+
 export interface ToolType {
   id: string;
   name: string;
   display_name: string;
   description: string | null;
-  compose_template: string;
+  category: string;
+  interfaces: string[];
+  default_port: number | null;
+  definition_type: 'compose' | 'dockerfile';
+  compose_template: string | null;
+  dockerfile_template: string | null;
+  build_context: Record<string, string> | null;
+  readiness_probe: ReadinessProbe | null;
   required_variables: string[];
   is_builtin: boolean;
   created_by_id: string | null;
@@ -17,14 +30,28 @@ export interface CreateToolTypeRequest {
   name: string;
   display_name: string;
   description?: string;
-  compose_template: string;
+  category?: string;
+  interfaces?: string[];
+  default_port: number;
+  definition_type?: 'compose' | 'dockerfile';
+  compose_template?: string;
+  dockerfile_template?: string;
+  build_context?: Record<string, string>;
+  readiness_probe?: ReadinessProbe;
   required_variables: string[];
 }
 
 export interface UpdateToolTypeRequest {
   display_name?: string;
   description?: string;
+  category?: string;
+  interfaces?: string[];
+  default_port?: number;
+  definition_type?: 'compose' | 'dockerfile';
   compose_template?: string;
+  dockerfile_template?: string;
+  build_context?: Record<string, string>;
+  readiness_probe?: ReadinessProbe;
   required_variables?: string[];
 }
 
@@ -51,3 +78,8 @@ export const updateToolType = async (id: string, data: UpdateToolTypeRequest): P
 export const deleteToolType = async (id: string): Promise<void> => {
   await apiClient.delete(`/tool-types/${id}`);
 };
+
+export const validateToolType = async (id: string): Promise<{ valid: boolean; errors?: string[] }> => {
+  const response = await apiClient.get<{ valid: boolean; errors?: string[] }>(`/tool-types/${id}/validate`);
+  return response.data;
+};

apps/web/src/components/app-shell.tsx

@@ -1,19 +1,61 @@
+import { useCallback, useEffect } from "react";
 import { Link, NavLink, Outlet } from "react-router-dom";
 
+import { getUserSessions } from "../api/sessions";
+import type { Session } from "../api/sessions";
 import { useTheme } from "../hooks/use-theme";
 import { useAuth } from "../state/auth";
+import { useSessions } from "../state/sessions";
+import { Icon } from "./icon";
+import type { IconName } from "../utils/icons";
 
-const NAV_ITEMS = [
-  { to: "/", label: "Dashboard" },
-  { to: "/projects", label: "Projects" },
-  { to: "/ssh-keys", label: "SSH Keys" },
-  { to: "/tool-types", label: "Tool Types" },
-  { to: "/settings", label: "Settings" }
+const NAV_ITEMS: { to: string; label: string; icon: IconName }[] = [
+  { to: "/", label: "Home", icon: "dashboard" },
+  { to: "/projects", label: "Projects", icon: "projects" },
+  { to: "/tool-workshop", label: "Tool Workshop", icon: "settings" },
+  { to: "/settings", label: "Settings", icon: "settings" }
 ];
 
+const SessionItem = ({ session }: { session: Session }) => {
+  const isRunning = session.status === "running";
+
+  return (
+    <a
+      href={session.url ?? `/projects/${session.project_id}`}
+      target={session.url ? "_blank" : undefined}
+      rel={session.url ? "noopener noreferrer" : undefined}
+      className="nav-item session-item"
+      title={`${session.display_name} (${session.status})`}
+    >
+      <span className={`session-status ${isRunning ? "running" : ""}`} />
+      <Icon name={session.tool_icon as IconName} size="sm" />
+      <span className="session-name">{session.display_name}</span>
+    </a>
+  );
+};
+
 export const AppShell = () => {
   useTheme();
   const { user, logout } = useAuth();
+  const { sessions, setAllSessions } = useSessions();
+
+  const loadSessions = useCallback(async () => {
+    try {
+      const data = await getUserSessions();
+      setAllSessions(data);
+    } catch {
+      // Silently fail - sessions are optional
+    }
+  }, [setAllSessions]);
+
+  useEffect(() => {
+    void loadSessions();
+    // Poll every 10 seconds
+    const interval = setInterval(() => {
+      void loadSessions();
+    }, 10000);
+    return () => clearInterval(interval);
+  }, [loadSessions]);
 
   return (
     <div className="shell">
@@ -32,6 +74,7 @@ export const AppShell = () => {
             }}
             type="button"
           >
+            <Icon name="logout" size="sm" />
             Logout
           </button>
         </div>
@@ -39,16 +82,34 @@ export const AppShell = () => {
 
       <div className="shell-body">
         <aside className="shell-nav" aria-label="Primary navigation">
-          {NAV_ITEMS.map((item) => (
-            <NavLink
-              key={item.to}
-              to={item.to}
-              className={({ isActive }) => (isActive ? "nav-item nav-item-active" : "nav-item")}
-              end={item.to === "/"}
-            >
-              {item.label}
-            </NavLink>
-          ))}
+          {NAV_ITEMS.map((item) => {
+            const isHome = item.to === "/";
+            const activeCount = sessions.filter((s) => s.status === "running").length;
+            return (
+              <NavLink
+                key={item.to}
+                to={item.to}
+                className={({ isActive }) => (isActive ? "nav-item nav-item-active" : "nav-item")}
+                end={item.to === "/"}
+              >
+                <Icon name={item.icon} size="sm" />
+                {item.label}
+                {isHome && activeCount > 0 && (
+                  <span className="nav-badge">{activeCount}</span>
+                )}
+              </NavLink>
+            );
+          })}
+          
+          {sessions.length > 0 && (
+            <>
+              <div className="nav-divider" />
+              <div className="nav-section-title">Live sessions</div>
+              {sessions.map((session) => (
+                <SessionItem key={session.id} session={session} />
+              ))}
+            </>
+          )}
         </aside>
 
         <main className="shell-content">

apps/web/src/components/code-editor.tsx

@@ -0,0 +1,56 @@
+import React, { useEffect } from "react";
+import Editor from "react-simple-code-editor";
+import { highlightCode, loadLanguage } from "../utils/language";
+
+interface CodeEditorProps {
+  value: string;
+  onChange: (value: string) => void;
+  language: string;
+  readOnly?: boolean;
+}
+
+export const CodeEditor: React.FC<CodeEditorProps> = ({
+  value,
+  onChange,
+  language,
+  readOnly = false,
+}) => {
+  useEffect(() => {
+    const highlight = async () => {
+      await loadLanguage(language);
+    };
+    void highlight();
+  }, [language]);
+
+  const hightlightWithLineNumbers = (input: string) =>
+    input
+      .split("\n")
+      .map(
+        (line, i) =>
+          `<div class="editor-line"><span class="editor-line-number">${
+            i + 1
+          }</span><span class="editor-line-content">${highlightCode(
+            line || " ",
+            language
+          )}</span></div>`
+      )
+      .join("");
+
+  return (
+    <div className="code-editor">
+      <Editor
+        value={value}
+        onValueChange={onChange}
+        highlight={hightlightWithLineNumbers}
+        padding={0}
+        className="editor-textarea"
+        textareaClassName="editor-textarea-input"
+        readOnly={readOnly}
+        style={{
+          fontFamily: '"Fira Code", "Monaco", "Courier New", monospace',
+          fontSize: 14,
+        }}
+      />
+    </div>
+  );
+};

apps/web/src/components/commit-dialog.tsx

@@ -0,0 +1,159 @@
+import React, { useState } from "react";
+
+import { Icon } from "./icon";
+
+interface CommitDialogProps {
+  isOpen: boolean;
+  filePath: string;
+  originalContent: string;
+  newContent: string;
+  onCommit: (message: string) => Promise<void>;
+  onCancel: () => void;
+}
+
+export const CommitDialog: React.FC<CommitDialogProps> = ({
+  isOpen,
+  filePath,
+  originalContent,
+  newContent,
+  onCommit,
+  onCancel,
+}) => {
+  const [message, setMessage] = useState("");
+  const [loading, setLoading] = useState(false);
+  const [error, setError] = useState(">");
+
+  if (!isOpen) return null;
+
+  const generateDiff = () => {
+    const originalLines = originalContent.split("\n");
+    const newLines = newContent.split("\n");
+    const maxLines = Math.max(originalLines.length, newLines.length);
+    const diff: { type: "same" | "added" | "removed"; line: string; lineNum: number }[] = [];
+
+    for (let i = 0; i < maxLines; i++) {
+      const original = originalLines[i] || "";
+      const updated = newLines[i] || "";
+
+      if (original === updated) {
+        diff.push({ type: "same", line: updated, lineNum: i + 1 });
+      } else {
+        if (original) {
+          diff.push({ type: "removed", line: original, lineNum: i + 1 });
+        }
+        if (updated) {
+          diff.push({ type: "added", line: updated, lineNum: i + 1 });
+        }
+      }
+    }
+
+    return diff;
+  };
+
+  const handleCommit = async () => {
+    if (!message.trim()) {
+      setError("Please enter a commit message");
+      return;
+    }
+
+    setLoading(true);
+    setError("");
+    try {
+      await onCommit(message);
+    } catch {
+      setError("Failed to commit changes");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  const diff = generateDiff();
+  const hasChanges = diff.some((d) => d.type !== "same");
+
+  return (
+    <div className="dialog-overlay">
+      <div className="commit-dialog">
+        <div className="dialog-header">
+          <h3>Commit Changes</h3>
+          <button className="dialog-close" onClick={onCancel} type="button">
+            ×
+          </button>
+        </div>
+
+        <div className="dialog-body">
+          <p className="file-info">
+            Editing: <strong>{filePath}</strong>
+          </p>
+
+          {!hasChanges && (
+            <div className="warning-message">No changes to commit</div>
+          )}
+
+          {hasChanges && (
+            <div className="diff-preview">
+              <h4>Changes</h4>
+              <div className="diff-content">
+                {diff.map((line, i) => (
+                  <div
+                    key={i}
+                    className={`diff-line diff-${line.type}`}
+                  >
+                    <span className="diff-line-number">{line.lineNum}</span>
+                    <span className="diff-marker">
+                      {line.type === "added" && "+"}
+                      {line.type === "removed" && "-"}
+                      {line.type === "same" && " "}
+                    </span>
+                    <span className="diff-line-content">{line.line}</span>
+                  </div>
+                ))}
+              </div>
+            </div>
+          )}
+
+          <div className="form-group">
+            <label>Commit Message *</label>
+            <textarea
+              value={message}
+              onChange={(e) => setMessage(e.target.value)}
+              placeholder="Describe your changes..."
+              rows={3}
+              className="form-textarea"
+            />
+          </div>
+
+          {error && <div className="error-message">{error}</div>}
+        </div>
+
+        <div className="dialog-footer">
+          <button
+            className="btn-secondary"
+            onClick={onCancel}
+            type="button"
+          >
+            <Icon name="cancel" size="sm" />
+            Cancel
+          </button>
+          <button
+            className="btn-primary"
+            onClick={handleCommit}
+            disabled={loading || !hasChanges || !message.trim()}
+            type="button"
+          >
+            {loading ? (
+              <>
+                <Icon name="loading" size="sm" />
+                Committing...
+              </>
+            ) : (
+              <>
+                <Icon name="commit" size="sm" />
+                Commit Changes
+              </>
+            )}
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+};

apps/web/src/components/commit-panel.tsx

@@ -0,0 +1,102 @@
+import { useState } from "react";
+
+import { commitChanges } from "../api/git_repositories";
+
+interface CommitPanelProps {
+  projectId: string;
+  repoId: string;
+  modified: string[];
+  added: string[];
+  deleted: string[];
+  untracked: string[];
+  onCommit: () => void;
+}
+
+export const CommitPanel = ({
+  projectId,
+  repoId,
+  modified,
+  added,
+  deleted,
+  untracked,
+  onCommit,
+}: CommitPanelProps) => {
+  const [message, setMessage] = useState("");
+  const [loading, setLoading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+
+  const allFiles = [...modified, ...added, ...deleted, ...untracked];
+  const hasChanges = allFiles.length > 0;
+
+  const handleCommit = async () => {
+    if (!message.trim()) {
+      setError("Please enter a commit message");
+      return;
+    }
+    setLoading(true);
+    setError(null);
+    try {
+      await commitChanges(projectId, repoId, message);
+      setMessage("");
+      onCommit();
+    } catch {
+      setError("Commit failed. Please try again.");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  if (!hasChanges) return null;
+
+  return (
+    <div className="commit-panel">
+      <h4>Changes</h4>
+      
+      <div className="file-list">
+        {modified.map((file) => (
+          <div key={file} className="file-item modified">
+            <span className="file-status">M</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+        {added.map((file) => (
+          <div key={file} className="file-item added">
+            <span className="file-status">A</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+        {deleted.map((file) => (
+          <div key={file} className="file-item deleted">
+            <span className="file-status">D</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+        {untracked.map((file) => (
+          <div key={file} className="file-item untracked">
+            <span className="file-status">?</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+      </div>
+
+      <div className="commit-form">
+        <textarea
+          placeholder="Commit message"
+          value={message}
+          onChange={(e) => setMessage(e.target.value)}
+          rows={2}
+          className="commit-message-input"
+        />
+        {error && <div className="commit-error">{error}</div>}
+        <button
+          onClick={handleCommit}
+          disabled={loading || !message.trim()}
+          className="commit-button"
+          type="button"
+        >
+          {loading ? "Committing..." : "Commit"}
+        </button>
+      </div>
+    </div>
+  );
+};

apps/web/src/components/file-editor.tsx

@@ -0,0 +1,241 @@
+import React, { useCallback, useEffect, useState } from "react";
+import { useSearchParams } from "react-router-dom";
+import { apiClient } from "../api/client";
+import { useAuth } from "../state/auth";
+import { CodeEditor } from "../components/code-editor";
+import { CommitDialog } from "../components/commit-dialog";
+import { Icon } from "../components/icon";
+import { SyntaxHighlighter } from "../components/syntax-highlighter";
+import { detectLanguage } from "../utils/language";
+
+interface FileEditorProps {
+  projectId: string;
+  repoId: string;
+}
+
+export const FileEditor: React.FC<FileEditorProps> = ({
+  projectId,
+  repoId,
+}) => {
+  const [searchParams] = useSearchParams();
+  const { user } = useAuth();
+
+  const [mode, setMode] = useState<"view" | "edit">("view");
+  const [content, setContent] = useState(">");
+  const [originalContent, setOriginalContent] = useState(">");
+  const [language, setLanguage] = useState("plaintext");
+  const [loading, setLoading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [showCommitDialog, setShowCommitDialog] = useState(false);
+  const [isBinary, setIsBinary] = useState(false);
+  const [saving, setSaving] = useState(false);
+
+  const branch = searchParams.get("branch") || "main";
+  const filePath = searchParams.get("file");
+
+  const loadFile = useCallback(async () => {
+    if (!filePath) {
+      setContent("");
+      setOriginalContent("");
+      return;
+    }
+
+    setLoading(true);
+    setError(null);
+    try {
+      const response = await apiClient.get(
+        `/projects/${projectId}/repositories/${repoId}/files/content`,
+        {
+          params: {
+            branch,
+            path: filePath,
+          },
+        }
+      );
+      const data = response.data;
+      if (data.is_binary) {
+        setIsBinary(true);
+        setContent("Binary file - cannot display");
+        setOriginalContent("");
+      } else {
+        setIsBinary(false);
+        setContent(data.content);
+        setOriginalContent(data.content);
+        setLanguage(detectLanguage(filePath));
+      }
+    } catch {
+      setError("Failed to load file");
+    } finally {
+      setLoading(false);
+    }
+  }, [projectId, repoId, branch, filePath]);
+
+  useEffect(() => {
+    void loadFile();
+  }, [loadFile]);
+
+  const handleEdit = () => {
+    if (isBinary) return;
+    setMode("edit");
+  };
+
+  const handleCancel = () => {
+    setContent(originalContent);
+    setMode("view");
+    setShowCommitDialog(false);
+  };
+
+  const handleSave = () => {
+    if (content === originalContent) {
+      setMode("view");
+      return;
+    }
+    setShowCommitDialog(true);
+  };
+
+  const handleCommit = async (message: string) => {
+    if (!filePath || !user) return;
+
+    setSaving(true);
+    try {
+      await apiClient.post(
+        `/projects/${projectId}/repositories/${repoId}/files/content`,
+        {
+          path: filePath,
+          branch,
+          content,
+          commit_message: message,
+          author_name: user.name || "User",
+          author_email: user.email || "user@example.com",
+        }
+      );
+      setOriginalContent(content);
+      setMode("view");
+      setShowCommitDialog(false);
+    } catch {
+      setError("Failed to save changes");
+    } finally {
+      setSaving(false);
+    }
+  };
+
+  // Keyboard shortcuts
+  useEffect(() => {
+    const handleKeyDown = (e: KeyboardEvent) => {
+      if ((e.ctrlKey || e.metaKey) && e.key === "e") {
+        e.preventDefault();
+        if (mode === "view" && !isBinary) {
+          handleEdit();
+        } else if (mode === "edit") {
+          handleCancel();
+        }
+      }
+      if ((e.ctrlKey || e.metaKey) && e.key === "s") {
+        e.preventDefault();
+        if (mode === "edit") {
+          handleSave();
+        }
+      }
+    };
+
+    window.addEventListener("keydown", handleKeyDown);
+    return () => window.removeEventListener("keydown", handleKeyDown);
+  }, [mode, isBinary, content, originalContent]);
+
+  if (!filePath) {
+    return (
+      <div className="file-viewer-empty">
+        <p className="muted">Select a file to view its contents</p>
+      </div>
+    );
+  }
+
+  if (loading) return <p className="muted">Loading file...</p>;
+  if (error) return <p className="error-text">{error}</p>;
+
+  return (
+    <div className="file-editor">
+      <div className="file-editor-toolbar">
+        <div className="file-breadcrumbs">
+          {filePath.split("/").map((part, i, arr) => (
+            <span key={i}>
+              {part}
+              {i < arr.length - 1 && (
+                <span className="breadcrumb-sep">/</span>
+              )}
+            </span>
+          ))}
+        </div>
+        <div className="file-actions">
+          {mode === "view" && !isBinary && (
+            <button
+              className="btn-primary"
+              onClick={handleEdit}
+              type="button"
+            >
+              <Icon name="edit" size="sm" />
+              Edit
+            </button>
+          )}
+          {mode === "edit" && (
+            <>
+          <button
+            className="btn-primary"
+            onClick={handleSave}
+            disabled={content === originalContent || saving}
+            type="button"
+          >
+            {saving ? (
+              <>
+                <Icon name="loading" size="sm" />
+                Saving...
+              </>
+            ) : (
+              <>
+                <Icon name="save" size="sm" />
+                Save
+              </>
+            )}
+          </button>
+              <button
+                className="btn-secondary"
+                onClick={handleCancel}
+                type="button"
+              >
+                <Icon name="cancel" size="sm" />
+                Cancel
+              </button>
+            </>
+          )}
+        </div>
+      </div>
+
+      <div className="file-editor-content">
+        {mode === "view" && (
+          <SyntaxHighlighter
+            code={content}
+            language={language}
+            showLineNumbers={!isBinary}
+          />
+        )}
+
+        {mode === "edit" && (
+          <CodeEditor
+            value={content}
+            onChange={setContent}
+            language={language}
+          />
+        )}
+      </div>
+
+      <CommitDialog
+        isOpen={showCommitDialog}
+        filePath={filePath}
+        originalContent={originalContent}
+        newContent={content}
+        onCommit={handleCommit}
+        onCancel={() => setShowCommitDialog(false)}
+      />
+    </div>
+  );
+};