The Java Packager tool will evolve for JDK 9, making it aware of modules, allowing for example to package a module and all the modules it depends on.2
For example, the following command will create a outputJar.jar file with the content of the classesDir directory, and will set the myPackager.MainClass as the executable class of the jar file:
"The Java Packager Tool". Oracle Corporation. Retrieved 2017-07-31. https://docs.oracle.com/javase/8/docs/technotes/guides/deploy/packager.html ↩
"JEP 275: Modular Java Application Packaging". Oracle Corporation. Retrieved 2017-07-31. http://openjdk.java.net/jeps/275 ↩