enable pre-commit checks in CI (github Actions)

[elmjag]

Makes the repository pre-commit clean and enables automatic pre-commit checks on pull requests.

Files that are currently not passing some pre-commit checks, are added to exclude lists.

• autoflake: https://github.com/mxcube/mxcubecore/commit/44867cff5ecd498ed742e2d6284565749ed8a03c#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R65
• black: https://github.com/mxcube/mxcubecore/commit/b0d492ac782218c103446d1e6bd1d791bf7dca52#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R132
• trailing-whitespace: https://github.com/mxcube/mxcubecore/commit/877c85e5d26486e61f8dd770fa0c04a71a76d5f4#diff-63a9c44a44acf85fea213a857769990937107cf072831e1a26808cfde9d096b9L31
• end-of-file-fixer: https://github.com/mxcube/mxcubecore/commit/13a9116d7cb51dc46641cbf66e2ba87c708c0f80#diff-63a9c44a44acf85fea213a857769990937107cf072831e1a26808cfde9d096b9R52

With this PR, we can keep all currently non-excluded and new files pre-commit clean using CI. Also, this gives us an option to to fix currently excluded files via small batches.

For small number of files, where changing formatting seems safe, I have applied white space fixes. This is some general config- and doc-files.