Apple - How to repair and/or reinstall Homebrew safely?

This happened to me because I had two tabs open in my console. In Console A I removed the current working directory of Console B. Then, without thinking about it, I ran brew upgrade in Console B. Of course it threw the above error.

Simple solution: just cd to a different directory in Console B and brew upgrade again.

Me and my infinite wisdom.

Why don't you do what it says?

rm -rf /usr/local/Cellar /usr/local/.git && brew cleanup
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

The first line is going to delete homebrew completely and then you should be able to reinstall it.

NOTE: If you do this you'll have to reinstall all the things you installed via homebrew.