Xcode aren’t keen when deleting files or directory without it being notifies and there refused to commit which is a pain. What worked to fix it was to recreate an empty folder with the same name. No need to recreate its contents.
After you committed you can delete the folder and commit again. Xcode is missing some kind of logic to handle the deletion of a whole folder with contents it seems in some situations sadly.
If this fails though try the folowing. If you’d like to simply commit all changes you made, doing so through the Terminal should fix the problem.
Open the Terminal App and cd into your project directory, once there type in the following command:
git commit -a
Enter your commit message by pressing ‘i’ and typing it in, then press ‘Esc’, then ‘:’, and type ‘wq’
All done, you’re problem should be fixed.