Building a web app (actually within a J2EE App)...
I have dependencies on 2 java modules.
In the Web Module settings, I have selected "jar module output and copy files to" and the path defaults to the obvious place, putting a jar based on the java modules name underneath the WEB-INF/lib. Looks good to me.
When I build, however, I see that it not only built the jar and put it under WEB-INF/lib, but it also copied all the classes under WEB-INF/classes.
This is in 5.1.1.