Add pre-commit hooks

[terhorstd]

Preparatory work for #3848:

• add more linters to .pre-commit-config.yaml → tool coverage
• configure tools to actually scan all files → file coverage
• keeps failing tests minimal, but fixes smaller problems → base issue coverage

After this PR we can start to remove the ignores one by one and proceed with #3848.

[heplesser]

Thanks for starting this. But the checks seem to generate insane numbers of false positives, likely due to the rather convoluted way in which we construct the nest module. Also, coverage seems to include the test files themselves, which seems counterproductive.