The guide at https://github.com/yepher/littlebits/blob/master/CloubitFileSystem.md is mostly correct but has a few mistakes. Luckily I found this page in Japanese http://qiita.com/chobie@github/items/d41cfa2d60df5d7d1a3f (and I can read Japanese) to point me in the right direction for the right way to do this.
Note: I used an Ubuntu linux machine to mount and edit the microsdcard.
You should also make a backup image of the SD card just in case.