There is hardcoded src/ folder in plugin.jelly during repackage. Is it bug or feature? For not standard templates it should be possible to set maven.genapp.repackage property also to folders not included in src/ (multiproject for example or unusual settings).
For example:
maven.genapp.repackage=src/java,test/java
Fixed, by using maven.genapp.repackage.dir instead of hardcoded 'src'.