While I do see a "META-INF" folder with an application.xml file in it, I do not see a "WebContent" folder housing this META-INF folder. So I really don't think this project is a well-formed EAR project.
I would need to see a copy of your {project}/.settings/org.eclipse.wst.common.component file to verify this though. But from the looks of it, I doubt sincerely there is a mapping of any sort for this project to actually include the META-INF folder in the final ear project.