Changes to the pre-commit setup

[egeakman]

Post-merge review (I was travelling last week): looks good :)

Only suggestions I would have made:

• keep check-toml
• put ruff-pre-commit first (because it might fix some things so pre-commit-hooks doesn't need to complain about them, and see the note at https://github.com/astral-sh/ruff-pre-commit about putting it before other formatters when using --fix
• move the Ruff args out of pre-commit config and into pyproject.toml, so they are available when running Ruff outside of pre-commit

But not a big deal.

Originally posted by @hugovk in #23 (review)