Migration from Docker to Standalone Python Server (#73)

* Migration from docker to standalone server
Migration handling
Fixed tests
Use simpler in-memory storage
Support for concurrent logging to disk
Simplified direct connections to localhost

* Migration from docker / redis to standalone script
Updated tests
Updated run script
Fixed requirements
Use dotenv
Ask if user would like to install MCP in Claude Desktop once
Updated docs

* More cleanup and references to docker removed

* Cleanup

* Comments

* Fixed tests

* Fix GitHub Actions workflow for standalone Python architecture

- Install requirements-dev.txt for pytest and testing dependencies
- Remove Docker setup from simulation tests (now standalone)
- Simplify linting job to use requirements-dev.txt
- Update simulation tests to run directly without Docker

Fixes unit test failures in CI due to missing pytest dependency.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Remove simulation tests from GitHub Actions

- Removed simulation-tests job that makes real API calls
- Keep only unit tests (mocked, no API costs) and linting
- Simulation tests should be run manually with real API keys
- Reduces CI costs and complexity

GitHub Actions now only runs:
- Unit tests (569 tests, all mocked)
- Code quality checks (ruff, black)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Fixed tests

* Fixed tests

---------

Co-authored-by: Claude <noreply@anthropic.com>

docker-compose.yml

@@ -1,81 +0,0 @@
-services:
-  redis:
-    image: redis:7-alpine
-    container_name: zen-mcp-redis
-    restart: unless-stopped
-    stop_grace_period: 3s
-    ports:
-      - "6379:6379"
-    volumes:
-      - redis_data:/data
-    command: redis-server --save 60 1 --loglevel warning --maxmemory 512mb --maxmemory-policy allkeys-lru
-    deploy:
-      resources:
-        limits:
-          memory: 1G
-        reservations:
-          memory: 128M
-
-  zen-mcp:
-    build: .
-    image: zen-mcp-server:latest
-    container_name: zen-mcp-server
-    restart: unless-stopped
-    stop_grace_period: 5s
-    depends_on:
-      - redis
-    environment:
-      - GEMINI_API_KEY=${GEMINI_API_KEY:-}
-      - OPENAI_API_KEY=${OPENAI_API_KEY:-}
-      - XAI_API_KEY=${XAI_API_KEY:-}
-      # OpenRouter support
-      - OPENROUTER_API_KEY=${OPENROUTER_API_KEY:-}
-      - CUSTOM_MODELS_CONFIG_PATH=${CUSTOM_MODELS_CONFIG_PATH:-}
-      # Custom API endpoint support (for Ollama, vLLM, etc.)
-      - CUSTOM_API_URL=${CUSTOM_API_URL:-}
-      - CUSTOM_API_KEY=${CUSTOM_API_KEY:-}
-      - CUSTOM_MODEL_NAME=${CUSTOM_MODEL_NAME:-llama3.2}
-      - DEFAULT_MODEL=${DEFAULT_MODEL:-auto}
-      - DEFAULT_THINKING_MODE_THINKDEEP=${DEFAULT_THINKING_MODE_THINKDEEP:-high}
-      - CONVERSATION_TIMEOUT_HOURS=${CONVERSATION_TIMEOUT_HOURS:-3}
-      - MAX_CONVERSATION_TURNS=${MAX_CONVERSATION_TURNS:-20}
-      # Model usage restrictions
-      - OPENAI_ALLOWED_MODELS=${OPENAI_ALLOWED_MODELS:-}
-      - GOOGLE_ALLOWED_MODELS=${GOOGLE_ALLOWED_MODELS:-}
-      - XAI_ALLOWED_MODELS=${XAI_ALLOWED_MODELS:-}
-      - REDIS_URL=redis://redis:6379/0
-      # Use HOME not PWD: Claude needs access to any absolute file path, not just current project,
-      # and Claude Code could be running from multiple locations at the same time
-      - WORKSPACE_ROOT=${WORKSPACE_ROOT:-${HOME}}
-      # USER_HOME helps detect and protect against scanning the home directory root
-      - USER_HOME=${HOME}
-      - LOG_LEVEL=${LOG_LEVEL:-DEBUG}
-      - PYTHONUNBUFFERED=1
-    volumes:
-      - ${WORKSPACE_ROOT:-${HOME}}:/workspace:ro
-      - mcp_logs:/tmp  # Shared volume for logs
-      - /etc/localtime:/etc/localtime:ro
-    stdin_open: true
-    tty: true
-    entrypoint: ["python"]
-    command: ["server.py"]
-
-  log-monitor:
-    build: .
-    image: zen-mcp-server:latest
-    container_name: zen-mcp-log-monitor
-    restart: unless-stopped
-    stop_grace_period: 3s
-    depends_on:
-      - zen-mcp
-    environment:
-      - PYTHONUNBUFFERED=1
-    volumes:
-      - mcp_logs:/tmp  # Shared volume for logs
-      - /etc/localtime:/etc/localtime:ro
-    entrypoint: ["python"]
-    command: ["log_monitor.py"]
-
-volumes:
-  redis_data:
-  mcp_logs: