[codex] 增加 MCP 工具档位和命令守卫

[catoncat]

Summary

• add configurable MCP tool profile support (full by default, optional read-only)
• add optional command guard for shell tools (off by default, with warn / block modes)
• persist run_command_stream stdout/stderr incrementally while background tasks are still running
• update docs and env examples for the new configuration

Validation

• ./.venv/bin/pytest -q -> 150 passed, 2 warnings
• ./scripts/launchd-reload.sh completed successfully
• local MCP endpoint http://127.0.0.1:8766/mcp returned 204
• public MCP endpoint https://notion-mcp.138000.xyz/mcp returned HTTP/2 204

Note: existing unrelated local dirty files were left out of this branch (cloudflared-example.yml, scripts/launchd-doctor.sh, scripts/launchd-status.sh).