If there is no application.xml, why not just assume every top level file is a deployment context and deployable if it doesn't have the ".jar" extension? We still are following the JavaEE5 ear rules, but can stuff in things like -beans.xml files and -ds.xml files at the top level and not require an application.xml file.
Then why not add a VirtualFileFilter that defaults to this behavior that is used when there is no app xml. I still think we need to scan jars for annotations to further filter out those that should not be included to be fully ee5 compliant.