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>

utils/__init__.py

@@ -4,7 +4,7 @@ Utility functions for Zen MCP Server
 
 from .file_types import CODE_EXTENSIONS, FILE_CATEGORIES, PROGRAMMING_EXTENSIONS, TEXT_EXTENSIONS
 from .file_utils import expand_paths, read_file_content, read_files
-from .security_config import EXCLUDED_DIRS, SECURITY_ROOT
+from .security_config import EXCLUDED_DIRS
 from .token_utils import check_token_limit, estimate_tokens
 
 __all__ = [
@@ -15,7 +15,6 @@ __all__ = [
     "PROGRAMMING_EXTENSIONS",
     "TEXT_EXTENSIONS",
     "FILE_CATEGORIES",
-    "SECURITY_ROOT",
     "EXCLUDED_DIRS",
     "estimate_tokens",
     "check_token_limit",