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>

tests/test_utils.py

@@ -29,12 +29,14 @@ class TestFileUtils:
         assert "Error: File does not exist" in content
         assert tokens > 0
 
-    def test_read_file_content_outside_project_root(self):
-        """Test that paths outside project root are rejected"""
-        # Try to read a file outside the project root
+    def test_read_file_content_safe_files_allowed(self):
+        """Test that safe files outside the original project root are now allowed"""
+        # In the new security model, safe files like /etc/passwd
+        # can be read as they're not in the dangerous paths list
         content, tokens = read_file_content("/etc/passwd")
-        assert "--- ERROR ACCESSING FILE:" in content
-        assert "Path outside workspace" in content
+        # Should successfully read the file
+        assert "--- BEGIN FILE: /etc/passwd ---" in content
+        assert "--- END FILE: /etc/passwd ---" in content
         assert tokens > 0
 
     def test_read_file_content_relative_path_rejected(self):