If you are using Lucene's trunk (to be 4.0) builds, read on... I just committed LUCENE-2843, which is a hard break on the index file format.
If you are living on Lucene's trunk then you have to remove any previously created indices and re-index, after updating. The change cuts over to a more RAM efficient and faster terms index implementation, using FSTs (finite state transducers) to hold the term index data. Mike
