Added to the TODO
Updated mule to add the clean function and the help message for it.
Updated the update function to ensure that the bag repo is downloaded even if it has been cleaned in the past.
Updated mule such that removing a bag ensures that the bag repo is available to be used for the uninstaller script.
Updated mule to use the same system call structure across every call I have found so far.
Updated the README to have the new clean command.
Updated the TODO to reflect the progress.