JBoss Developer Studio doesn't generate application.xml correctly

Issue

• I have a Maven project using JBoss Developer Studio. During deployment the application.xml is not generated. Using command line maven tools works just fine.
• Using the menu to "Generate Deployment Descriptor Stub" only works once, then when you clean do a Maven/Update Project it is lost again. The generation of the application.xml is also not consistent as JAR's which are part of the EAR do not get included.