The mootools-filemanager is a git repository which (probably) contains local modifications to work better with Xinha. Therefore, we want to keep it as a git repo so we can easily update.
The upstream git repository is (from http://github.com/cpojer/mootools-filemanager)
git://github.com/cpojer/mootools-filemanager.git
Simply CD'ing into the mootools-filemanager directory and performing
git pull
should be sufficient to update.
The mootools-filemanager/.git/ directory should be stripped prior to shipping for space concerns.