I'd like to see a more flexible way to adjust the classpath entries in the manifest file. For example with the ear-plugin I'm able to put third party libraries to a different folder (e.g. lib/) than project module artifacts (e.g. root folder). For ejb-modules I need to be able to specify classpath entries for both folders (e.g. lib/log4j.jar and a.b.c.project-common.jar). As you can only specify a general prefix this layout is currently not handled.
Attached you find a patch against the trunk which introduces a new additional configuration option classpathPrefixThirdParty. Dependencies that have a different groupId from the project itself are prefixed with that option.