How to repair and/or reinstall Homebrew safely?

I am trying to repair Homebrew.

I recently tried to reinstall it but when I typed "brew doctor"

My output was:

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
The current working directory doesn't exist, cannot proceed.

I have tried to re-install it by typing this into the command line again:

ruby -e "$(curl -fsSL http://ift.tt/YQTuQh)"

But my output is:

It appears Homebrew is already installed. If your intent is to reinstall you
should do the following before running this installer again:
rm -rf /usr/local/Cellar /usr/local/.git && brew cleanup

How can I fix my Homebrew install?

Thank you.