Fix CI lint failures and modernize checks (mypy → pyrefly, pre-commit → prek)

[aadimator]

CI is currently failing on lint/type checks, so this issue tracks a cleanup pass to make our pipeline reliable again and simplify tooling.

What we’ll do

• Replace mypy with pyrefly across the project and CI
• Replace pre-commit with prek
• Fix current lint/type issues that are breaking CI
• Remove old config/docs references to mypy and pre-commit

Done when

• CI is green on PRs and main
• pyrefly and prek are the active tools everywhere
• Existing lint/type debt is resolved (or explicitly documented as follow-up)