Hi,
the best solution would be to use XML based configuration which can add/override the annotation based configuration. Unfortunately, there is no such XML based configuration yet. You find some hints on how to do this here -
http://www.hibernate.org/443.html. If you are interested in this approach let us know and we can help you out as much as can.
Of course you could just try to extend the configuration for your particular need, but that would of course not be generic anymore.
There exists also the possibility to access the Lucene resources directly -
http://www.hibernate.org/hib_docs/search/reference/en/html_single/#search-lucene-native. Depending on your use case it might be possible to modify the index yourself. However, I would not recommend this approach.
--Hardy