Assuming:

public class TopLevelClass
{
private static class InnerClass{}
}

...and:

getClassContainer().addClasses(TopLevelClass.class);
log.info(getArchive().toString(true));

...output is:

test@jboss:/$ ls -l f59005e3-0dcc-417e-84fd-2f35ab8ae18f.jar
f59005e3-0dcc-417e-84fd-2f35ab8ae18f.jar:
/org/jboss/shrinkwrap/impl/base/spec/TopLevelClass.class

This is especially problematic where the caller cannot access the inner class due to visibility constraints. It'll be missing from the runtime. Discuss the rules we should apply (regarding hierarchy) on the forum.