I too don't understand these long discussions. As the OP is painfully realizing, to maintain a Unix server these GUI tools are inadequate. Shell is the original and still the preferred too, In this case a combination of chown, chgrp, chmod and find would have solved the problem long ago. One must have a understanding of the basic Unix file permissions to translate the Moodle requirement "For Moodle to work you need to have the set of permissions that let Moodle read and write files, and list and enter (traverse) directories." to one's own environment.