[Answered ]-Overwriting folders with git

I think you’re over-thinking this. Ignore files you think you should (like *.pyc). Add all the files or do them individually, whichever you prefer. If you accidentally added one you shouldn’t have, do a checkout of that file so that you don’t add it. If you already committed with a file, git delete the file and commit.

You use git status, it will give you the list of all the files it’s currently not tracking, so you can use that as a reference if you’re afraid you’ll forget something.

Additionally, I would say that you don’t want to forget to properly setup your .gitignore, and then you can instruct git to add everything, otherwise, like Mark suggested, you would potentially be adding **.pyc* files, which you don’t want to do.