We are very happy that JabRef is part of Software Engineering trainings. Please head to Teaching for more information on using JabRef as a teaching object and on previous courses where JabRef was used.
The package org.jabref.cli is responsible for handling the command line options.
During development, one can configure IntelliJ to pass command line parameters:
Passing command line arguments using gradle is currently not possible as all arguments (such as -Dfile.encoding=windows-1252) are passed to the application.
Without jlink, it is not possible to generate a fat jar any more. During development, the capabilities of the IDE has to be used.