It seems that the HowToBuild wiki article on how to build JOGL has the wrong url for the git repository.
They should be this (I think? these worked)
git clone git://jogamp.org/srv/scm/gluegen.git gluegen
git clone git://jogamp.org/srv/scm/jogl.git jogl
These were from this page:
http://jogamp.org/jogl/doc/HowToBuild.htmlThey reference jogamp.com instead of jogamp.org
*edit: whoops. typo.