[BUG] Linting and code style checks should only be applied to files staged for commit

[mabolek]

Describe the bug
Currently, the entire repository is checked using the git pre-commit hook. This means commits will fail if you have a file with code style issues—even if it's not going to be committed. This means it is impossible to commit a completed file while you still have a work in progress elsewhere.

To Reproduce
Steps to reproduce the behavior:

1. Change a file so it won't pass code checks.
2. Change a different file, but make sure this change will pass code checks.
3. Stage the second file for commit with git add [filename]
4. Try to commit with git commit

The commit will fail.

Expected behavior
Committing should work.