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>

simulator_tests/test_line_number_validation.py

@@ -145,14 +145,16 @@ def validate_data(data):
             # Test 4: Validate log patterns
             self.logger.info("  1.4: Validating line number processing in logs")
 
-            # Get logs from container
-            result = self.run_command(
-                ["docker", "exec", self.container_name, "tail", "-500", "/tmp/mcp_server.log"], capture_output=True
-            )
-
-            logs = ""
-            if result.returncode == 0:
-                logs = result.stdout.decode()
+            # Get logs from server
+            try:
+                log_file_path = "logs/mcp_server.log"
+                with open(log_file_path) as f:
+                    lines = f.readlines()
+                    logs = "".join(lines[-500:])
+            except Exception as e:
+                self.logger.error(f"Failed to read server logs: {e}")
+                logs = ""
+                pass
 
             # Check for line number formatting patterns
             line_number_patterns = ["Line numbers for", "enabled", "│", "line number"]  # The line number separator