Hi Max,
yes I import my ear project as maven project. The application xml is under <project>/target/<artificat-id>/META-INF/.
I have two files under META-INF jboss-structure.xml and application.xml. But the JBoss tools plugin copies onlye the jboss-structure.xml into my deployment.
If I create a EarContent folder and copy the files manually or via maven profile like above then the application.xml stay in my deployment.