Thanks for everyone's input. This is what I finally got to work.
1. I backed up Contrib and created an empty Contrib folder with the same permissions.
2. I backed up Pending and created an empty Pending folder with the same permissions
3. I backed up .gitignore and ran "git checkout .gitignore"
4. I updated the OPL by the usual commands.
This seemed to work.
Note: I tried backing up the OpenPublicLibrary and creating an empty OpenPublicLibrary folder then running "git pull" and updating but something went wrong and I had to reinstall the backed up folder and update again. Not sure what happened there. Anyway, I hope this helps someone else and always remember CREATE BACKUPS OF FOLDERS AND FILES BEFORE MESSING WITH YOUR SYSTEM!