Currently the JOGL build process depends on the gluegen directory being available.
As part of the packaging of JOGL and JOAL for gentoo. I have started to separate
gluegen from the 2 packages build environment.
Basically the main patch just adds conditional checks so that if the properties
gluegen.jar and gluegen-rt.jar are avaliable files the gluegen build process is
skipped. Hopefully this will allow a compromise between your needs and those of
opensource projects wishing to package JOGL.
Secondly I noticed that you depend on an old version of cputasks. Newer
versions do not seem to support the suncc compiler and this patch just changes
those values to gcc. this patch might not be suitable for you.