Expand ruff checks, and apply non-formatting checks to CI

[scal444]

No description provided.

[greptile-apps]

Confidence Score: 5/5

The PR appears safe to merge, with no outstanding correctness, security, or repository-rule violations identified.

Summary

This PR broadens Ruff’s configured lint categories and applies lint checks alongside formatting in CI.

• Updates the Ruff helper to run safe lint fixes locally and non-mutating checks in dry-run mode.
• Cleans up newly detected lint violations across the Python package, tests, and benchmarks.
• Preserves the order-sensitive native converter bootstrap sequence in nvmolkit/types.py.

_{Reviews (4) · Last reviewed commit: "Clarify native converter import ordering"}

[evasnow1992]

Changes look good to me. One non-blocker comment.