ci: GHA basic format & pre-commit

[henryiii]

Implementing basic GHA formatting. Changes:

• Pre-commit support. All checks except for C++ format (to be added later) are available in pre-commit instead of custom tools/check_style.sh - also checks flake8. Many of the old warnings are now automatic fixes.
• GitHub Actions checks pre-commit style
• Flake8: Added bugbear - manually fixed a few resulting "unused variable" warnings
• pre-commit: Added encoding & whitespace fixes to several files automatically

I added tab -> 4 space automatic conversion, but there's also a mode that simply errors on any tabs. You always get to review changes with pre-commit before adding them in git, so automatic is usually better, but we could use the other mode for tabs.