application.xml related stuff

I have been going nuts trying to trace problems with deployment of
enterprise applications and resource injection. I think the issue is
around the application.xml file in a .ear! Without an
application.xml file, everything is fine and dandy. As
soon as you add an application.xml file, things start
breaking... it seems that when you have defined an
application.xml file only those modules that are defined in
the application.xml file are loaded. Without a
application.xml file, all the .jar files are scanned for
@Stateless and @Statefull annotations and the
modules are inferred. It would help if there was some notification that
maybe your application.xml file was incomplete, or else
some way of restoring the scanning behaviour if you want it. Now to go
digging through the spec to see if I'm just stupidly missing something
or if I need to file a bug report.