docs: comprehensive documentation overhaul

Add complete documentation structure:
- Frontend architecture documentation
- Database schema documentation
- Deployment guides (Docker, Traefik, Authentik, Environment)
- Development guides (Setup, Testing, Contributing, Quality Gates)
- Deployment architecture documentation
- Updated docs README with complete navigation

All new features and APIs are now documented.
Quality gates: docs only, no code changes

docs/api/README.md

@@ -0,0 +1,51 @@
+# API Documentation
+
+## Overview
+
+The Headquarter API is a RESTful API built with FastAPI. All endpoints (except auth) require authentication via session cookie.
+
+## Base URL
+
+- Development: `http://localhost:8000`
+- Production: `https://api.yourdomain.com`
+
+## Authentication
+
+Most endpoints require authentication. Include the session cookie in requests:
+
+```bash
+curl http://api.example.com/endpoint \
+  -H "Cookie: session=your_session_cookie"
+```
+
+## Response Format
+
+All responses are JSON. Error responses follow this format:
+
+```json
+{
+  "detail": "Error message"
+}
+```
+
+## API Sections
+
+- [Auth](auth.md) - Authentication endpoints
+- [Projects](projects.md) - Project management
+- [Repositories](repositories.md) - Git repositories and file operations
+- [Users](users.md) - User management and settings
+- [Tool Types](tool-types.md) - Tool type management
+- [SSH Keys](ssh-keys.md) - SSH key management
+
+## Testing
+
+Interactive API documentation is available at `/docs` when running the backend:
+
+```
+http://localhost:8000/docs
+```
+
+This provides:
+- Interactive endpoint testing
+- Request/response schemas
+- Authentication via "Authorize" button