Hi,
Which files are in the lib folder? It’s containing the libraries necessary to run your sketch like gluegen, jogl and of course the core Processing library.
In fact I think that it always contains :
$ ls application.linux64/lib
core.jar gluegen-rt.jar jogl-all.jar
your_app.jar gluegen-rt-natives-linux-amd64.jar jogl-all-natives-linux-amd64.jar
(your_app.jar is the java archive of your sketch)
My guess is that you can’t delete the lib folder because those libraries are mandatory for the sketch to run. The source folder only contains the source of your program but it’s not the files that are directly used.
You can check this thread to find more information if you are exporting on Linux : How to export applications using Processing 3