Thanks! Philjord's recommendation was just what I needed.
As to gouessei's suggestion, I have a working Java3D app that I will be extending with pure jogl graphics. So, I don't want to do anything with the Java3D for now. I have a few months in which to work almost exclusively on this stuff, so I just wrote this little app to get back into the programming mindset. I will be writing another fairly simple jogl app next to work into that before I tackle the much more complicated integration of the jogl library Lili wrote for me a year or so ago.
I just finished reading the OpenGL Programming Guide 8th Ed. to become familiar with the lingo. Now, working through some simple online tutorials and the jogl online documentation/examples. I could hack away to get things to work, but I want to take this opportunity to build a more solid foundation.
Again, thanks for the help. I am sure I will be pestering more in the not-too-distant future.
You might still need one of my workarounds under Mac as Apple unfortunately goes on shipping old versions of Java3D with old versions of JOGL. Disabling the extension mechanism or using a JRE with no such feature (OpenJDK 1.9) just works :)
Hmm, as mentioned, I had largely forgotten about this. My users are scientists who should be able to at least run a script. However, in investigating further, I cannot find the old Java3D libraries on my Mac, and cannot remember the last time I moved them out of the search path. I am running OS X 10.11.6 (El Capitan). Might they have been removed from the more recent OS X distributions?
As to GPL, I am currently distributing source (see above) under the Apache 2.0 license, and plan doing the same for all future source releases. I really couldn't appreciate the differences between the various license options, so I picked Apache because I am already using their matrix algebra libraries and they seem to do an acceptable job with OpenOffice. Any reason I should not do so? Would that suffice for JNDT usage?
As far as I remember, Apple Java3D 1.3 and JOGL 1 were still under OS X 10.11, maybe you already removed them earlier.
The GPL is viral unlike the Apache 2.0 license. JNDT injects some parts of itself into the bundles which drives it unusable in non GPL programs. The choice of the license for your own code is entirely up to you. The GPL v3 is compatible with the Apache 2.0 license:
My desktop running 10.11.6 and my just-updated laptop running 10.12 do not have any of the old files. However, my friend, whom I am confident has upgraded to 10.12, shows the old files still in his /System/Library/Java/Extensions directory. All files are dated Jul 6 2015.
On my systems, I had run an app (provided to my users) that moved the troublesome files to a ./hold_j3d subdirectory off of the above, and to be a good citizen, there was also an app that undid the move. I suppose that the directory might have gotten deleted during subsequent upgrades, while my friend's upgrades retained all of the files in the original directory. Though, he has a number of non-related files I do not have. I only have MRJToolkit.jar.
Or might it be that installation of Java updates overwrites the directory? Checking with my friend for further info.
I don't think that Oracle Java overwrites any directory, it's the same for OpenJDK. If you don't want to move & "unmove" the libraries, just use a command line option in a script to override the extension path of the software instead of modifying your system.