What is the best/safest way to reinstall Homebrew?

Try running the command brew doctor and let us know what sort of output you get

edit: And to answer the title question, this is from their FAQ :

Homebrew doesn’t write files outside its prefix. So generally you can just rm -rf the folder you installed it in.

So following that up with a clean re-install (following their latest recommended steps) should be your best bet.

Update 10/11/2020 to reflect the latest brew changes.

Brew already provide a command to uninstall itself (this will remove everything you installed with Homebrew):

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh)"

If you failed to run this command due to permission (like run as second user), run again with sudo

Then you can install again:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

For Mac OS X Mojave and above

To Uninstall Homebrew, run following command:

sudo ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall)"

To Install Homebrew, run following command:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

And if you run into Permission denied issue, try running this command followed by install command again:

sudo chown -R $(whoami):admin /usr/local/* && sudo chmod -R g+rwx /usr/local/*

Process is to clean up and then reinstall with the following commands:

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

Notes:

Always check curl | bash (or ruby) commands before running them
http://brew.sh/ (for installation notes)
https://raw.githubusercontent.com/Homebrew/install/master/install (for clean up notes, see "Homebrew is already installed")

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