Are not optimized indices causing you any problems (e.g. slow searches, high number of open file handles)? If no, then you don't even need to optimize until those issues become... issues.
OK I have changed the process to not doing optimize() at all. So far so good. The number of files hover from 10 to 40 during the indexing of 10,000 files. Seems Lucene is doing some kind of self maintenance to keep things in order.
Is it right to say optimize() is a totally optional operation? I probably get the impression it is a natural step to end an incremental update from the IndexHTML example. Since it replicates the whole index it might be an overkill for many applications to do daily.
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