Refactor code structure for improved readability and maintainability

feat: expand `run_python` tool description for enhanced clarity and detail.

docs: Update Python Sandbox summary to emphasize persistence and state retention.

feat: document persistent sessions and execution, and add Terminal Bench references to README.

feat: Implement persistent code execution in the sandbox by processing commands via an stdin queue and add a new persistence test.

docs: Add link to OneMCP to the README.

feat: Add detailed server descriptions to `discovered_servers()` and refactor server discovery.

docs: Add comparisons to Speakeasy Dynamic Toolsets and Gentoro OneMCP in README.

docs: generalize MCP server registration instructions and simplify server discovery documentation.

feat: Add 'No-MCP' philosophy and robustness features to README, and refactor logging to be configurable via environment variable.

feat: Implement file-based debug logging and robust error handling for the main application loop.

feat: simplify config sources by limiting to MCPs directory and temporarily disable unused sources

feat: enhance Podman support by probing for existing shared volumes on older builds

feat: prevent recursive launches by skipping self-referential MCP server configurations and add environment variable support

feat: enhance error handling by ignoring benign JSON parse exceptions and improve test coverage for blank line scenarios