Hi Laird,
You should be able to override, but the association between the annotation and the .xml elements is based on the component environment name of the dependency. In the case of @PersistenceContext that means the name() attribute, which isn't specified in your example. If not specified, it defaults to <fully-qualified-name-of-declaring-class>/<field-name>. So, you'll either have to specify the name() attribute as
@PersistenceContext(name="persistence/FoobarPersistenceContext) to match the .xml
or
update the persistence-context-ref-name element to match the result of the default for the abstract class.
--ken
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