Improvements to format_check.py to reduce unintended changes

[IntegratedQuantum]

Common sources for unintended changes are empty lines and newlines at the end of the file.
Since some editors seem to require or at least prefer newlines at the end of files, it would make sense to standardize those.
As for empty lines some editors seem to place full indentation there, while others leave them empty.
I would say empty makes more sense, given that it's just simply less bytes, and also the default behavior in VSCode.

I would like to do this once the two big PRs are merged.