We've already seen a couple of issues like this:
- http://www.jboss.com/index.html?module=bb&op=viewtopic&p=4156755#4156755
- some Anil's security resources

In the first item, I very much doubt Seam users will want to write jboss-structure.xml file to make their jbpm, drools, ... files part of classpath.

Where all should this be applied - ear, ...?

In EARStructure it is probably this false that needs to be configurable?

 // Add the ear manifest locations?
 super.addClassPath(root, file, false, true, context);