As far as I remember, programmatic API creates Annotations (with AnnotationFactory) and works like you annotate your Entities in your source.

ex:

@MappedSuperclass 
public class Foo {
  @Basic
  public String foo;
}

@Entity 
public class Bar extends Foo {
  @Basic
  public String bar;
}

So you have to...

searchMapping.entity(Foo.class).property("foo", ElementType.FIELD).field(); 

searchMapping.entity(Bar.class).indexed().property("bar", ElementType.FIELD).field();

As far as I know, per Entity Mapping is currently not possible. So if you have another Entity, ex 'Baz extends Foo', Baz inherits Foo mappings. The same for Embeddable classes.

It would be a nice if programmatic API could manage inherited properties (from MapperSuperclass and Embeddable) per Entity... but I'm afraid that this is a big change...

Please feel free to clarify if I'm wrong.