Dumping some thoughts I had when editing this issue:

• First of, talking about @MappedSuperclass in this context is misleading. Really the problem is entities in class hierarchies and the fact that using the programmatic API you cannot configure properties of super types in the EntityMapping of the sub type. This is partly caused by the fact that the programmatic API creates proxy annotations on the entity.
• Regarding the proxy annotation problem. One way to solve the problem would be to allow the configuration of super type properties as part of the sub type EntityMapping. In this case we would need to process the class hierarchy when placing the proxy annotations and place it on the right class. IMO, this would be more consistent with the way annotations works anyways
• A better approach, however, could be to turns things around. The _DocumentBuilder_s should process _SearchMapping_s instead of annotations. The annotation processing/parsing could then create _SearchMapping_s. The benefit I see is that we get a clearer separation of the reading of the annotation vs using this information to configure the _DocumentBuilder_s. Annotation processing becomes a two step process. IMO a big advantage.