Is your suggestion for improvement related to a problem? Please describe.

I observe at least one package and even class name collision between two JabRef Modules:

org.jabref.cli.ArgumentProcessor exists in jabgui and jabkit and both classes are quite different. They have completely different members, so this is more than just a shadowing hack.
While technically possible, already the package name clash is bad style. So-called split packages are discouraged in the Java module system and can cause unforeseen issues.

From https://dev.java/learn/modules/intro/:

Packages should have a unique origin, so no two modules can contain types in the same package. If they do, this is called a split package, and the module system will refuse to compile or launch such configurations.

Describe the solution you'd like
Please refactor to avoid split packages as it is an unnecessary risk and source of trouble. The earlier this is done, the easier the change will be. I strongly recommend to adjust this before beta phase.