getAnnotatedClasses is for the usual EE annotations, some can be on field, method, type.
So, you don't care where it is? e.g. @RunAs on whole class vs. just on a method
In this case this signature will do:
/**
* Get annotated classes.
*
* @param cpEntry the classpath entry
* @param annotationToLookFor the annotation to look for
* @return set of annotated classes
*/
Set<Class<?>> getAnnotatedClasses(VirtualFile cpEntry, Class<? extends Annotation> annotationToLookFor);
Since you can do the merging/intersection/... yourself. ;-)