I ended up running sudo DIFFPROG=diff pacdiff and overwrote the files and I rebooted. After that I could not log in. Both my root and my user accounts password were rejected. I decided at that point to reinstall Manjaro Budgie (I have my /home in a different partition)
After doing so I was able to use sudo again, but the success was short lived. After I restored the .config/fish folder, and made fish my default editor with
chsh -s `which fish`
then logged out, the problem came back again. I’m assuming that is where the problem lies. I’ll update this when I find the problem & solution.