Python CLI Bug Fix: Preserve User Configuration

Problem: Omi's Python CLI could erase unrelated root settings from config.toml when a user updated a known setting. What I changed: I reproduced the loss with a synthetic configuration, then updated the configuration round-trip to retain unknown root scalars and tables while known fields remained authoritative. A regression test invokes the real omi config set command and checks that both the requested change and unrelated values survive. Verification: The contribution was reviewed and merged as PR #12990 on September 8, 2026. The original full CLI validation recorded 130 passing tests on Windows/Python 3.12. These are historical PR results, not a claim of a fresh production deployment. Source and review: https://github.com/BasedHardware/omi/pull/12990