I made a git repository in a main folder for a certain project to keep track of the entire project. But actually it was only keeping track of stuff in that main folder and a few of the subfolders. Other subfolders had separate git repos! I needed to get everything in one repo without screwing up any of my work. I will not go into the silly details of how this terrible situation arose, but if you happen to find yourself in this position, MiniQuark‘s answer to this question may save you some time.