Your abstract EJB is not processed for injection, not an abstract entity, right? If this is correct, persistence.xml won't help.... EJBContainer relies on the existing deployment code to deploy EJB module found on the classpath. The deployment code was always under assumption that what you deploy, is a complete module or application, and nothing outside of it should be looked at.
If there is more than 1 found, EJBContainer bootstrap code creates a temp ear with the corresponding modules, so that those modules can "see" each other. See if making an abstract class concrete, and adding e.g. @Stateless annotation, would help...
-marina
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