If a (EJB) deployment jar contains a MANIFEST.MF which points to another deployment (not a plain jar) through the ClassPath attribute, then the deployment framework does not generate metadata for the deployment listed in MANIFEST.MF

Ex: A.jar is an EJB3 deployment which contains a MANIFEST.MF pointing to B.jar (another EJB3 deployment). While processing A.jar (and its entries in MANIFEST.MF), the deployment framework does not generate metadata for B.jar

As per EJB3.0 core spec, section 20.3:

The ejb-jar file must contain, either by inclusion or by reference, the class files of each enterprise bean as follows:

• The enterprise bean class.
• The enterprise bean business interfaces, web service endpoint interfaces, and home and component interfaces.
• Interceptor classes.
• The primary key class if the bean is an entity bean.

We say that a jar file contains a second file "by reference" if the second file is named in the Class-Path attribute in the Manifest file of the referencing jar file or is contained (either by inclusion or by reference) in another jar file that is named in the Class-Path attribute in the Manifest file of the referencing jar file.