Git showing every changed file not folders
The difference between showing the folder level for untracked files and the file level for tracked files is expected git behavior. This will always be the case. Once you add the folder (which adds all the files in it) each of the files is tracked by git and will be tracked individually. So, when you do a status, it SHOULD list each file separately. Yes, this is kind of annoying, but the general idea is that you'll add a folder and then commit that change. Once committed, you won't see each file unless is has been changed in some way.

As for fixing the situation, you probably haven't actually messed anything up; it's just tough to see that because there are so many new files in your index (a git term which you can research if you'd like more information).

If you'd like to undo it all, you can run the git reset command. In general, most things related to git can be demystified with a couple of Google searches. If you're new to git, I recommend the free Git Book.