Some news on my side. The last problem seems to be linked with my JOGL dependencies.
Here are my jogl dependencies in pom.xml:
Let me detail step by step :
1 - First of all, everything works fine under eclipse (JOGL / CUDA). All works perfectly fine. The native libraries are somehow loaded and discovered correctly.
2 - I install my plugin to my local Fiji by using the mvn clean install command.
So far, so good.
3 - I launch Fiji.
4 - If I execute my plugin, I get the Null Pointer Exception mentioned above.
5 - I go to help > update. Here's what I found:
My plugin wants to remove platform specific jars for the general ones.
6 - I apply the suggested changes and restart ImageJ.
7 - I execute my plugin and ...
It works! (good, I don't get the Null Pointer Exception and some parts of the plugin start). Except when it needs JOGL... in this case, this error shows up :
java.lang.UnsatisfiedLinkError: Can't load library: /home/nico/natives/linux-amd64//libnativewindow_awt.so
Note that if I move the natives that are in the jar in Fiji.app>jars>linux64>jogl-all-2.3.2-natives-linux-amd64.jar to the indicated folder (/home/nico/natives/), then it works.
Of course, it would be better if there was a way to link my plugin directly to these natives.
How should I do that ?
PS1 : the source code of the plugin is here : https://github.com/NicoKiaru/LimeSeg
PS2 : I made an update site (NicoKiaru) with a benchmark that launches itself on the plugin call (if you want to repeat these steps)
PS3 : the topic is slightly drifting to a JOGL issue. I can open another thread if necessary.
Again, thanks for the nice support!