I think it's the most important sources of my cognitive dissonance around git. It strengthens the illusion that a working directly is somehow related to a git store, which it really isn't.

You have a working directly/checkout - that can be: identical (apart from ignored files) to some version in git; or different.

If it's different ; some or all changes can be marked for storing in the git repo - most commonly as a new commit.

It's a bit unfortunate that the repo typically is inside your work directory/checkout - under '.git' along with some files like hooks, that are not in the repo at all...