Update pre-commit hooks

[ndevenish]

Same as cctbx/dxtbx#403, mainly to get the new pre-commit-hook branch defaults changes. This will go back to "Disallow commit on main".

Rough guide to changes between these version:

• Isort: Mainly stability and configuration changes
• Black: Mainly internal restructuring, string and docstring edge-case handling
• flake8: Updated backend checkers
• pre-commit-hooks (things that affect us):
  • no-commit-to-branch: added "main" to default blocked branches <- the thing I wanted
  • check-added-large-files: added an --enforce-all option to check files already existing

Additionally, check-yaml fell over on .clang-format. We never ran this before because it hasn't been changed since we added the validation check. This needs you to explicitly request multi-document yamls, which has been added.

There are a few rogue flake8 issues with pre-commit run --all, but I have not changed them here.