We have an EJB project along with some custom assemblies:
This creates a test.jar and a test-custom.jar. The first jar has its Class-Path entry filled in correctly in the manifest file, but the 2nd jar has no Class-Path entry. The <addClasspath>true</addClasspath> was added for the maven assembly plugin, the maven-ejb-plugin in the parent pom also has this property set to true.
This only happens with maven 3.0.3. With maven 2.2.1 both jars have their Class-Path filled in properly.