I have a JSP module and a Java module - the JSP module depends on the Java module and the Java module exports some named module-level libraries.
In the JSP module I set the named library to "Copy files to ..." and save the config.
The next time that I start up the jsp.iml definition file has been changed and the library is set to "do not package".
To reproduce:
1) unzip the given project
2) copy the jsp.iml file somewhere safe
3) load the project into Idea
4) once the project has finished loading, compare the file jsp.iml with the copy that you made in step 2 - they are different
5) go to the module definition for JSP.iml, the library Logging is set to "do not package" and it should be "copy"
I put this as high because I have never really managed to get a stable JSP module definition since Idea 3.0 - but if this bug is fixed I think I'm finally there ...