The SU wizards create source project containing the directories "src/main/java".
If you add Java classes in this directory, they are not compiled on the fly and not packaged during the Petals export. To do this, you need to add the Java nature to the project (through the contextual menu: Petals/Add Java Nature).
It's ambiguous.
Because of majority of SU does not need Java classes, please remove the creation of directories "src/main/java" from SU wizards. On the add of Java nature, please add the directory creation, and all Java stuff activation.