How do I clear the command history in the mongo shell

MongoDB terminal history is stored inside the ~/.dbshellfile. Just empty the .dbshell file

 $ > ~/.dbshell

Versions of Windows mongo.exe earlier than 2.2.0 will save the .dbshell file in the mongo.exe working directory.

You can clear contents on the shell by Ctrl + L

There should be a file called .dbshell in your home folder. Just delete it.