Does this mean that if an IndexSearcher has hold of a segment file, then the index is optimised, any subsequent search will use a list of files that probably don't exist anymore?
The IndexSearcher (through an IndexReader) has the files open, so it is still valid, and may be searched. On Unix, the may have already been deleted, since Unix lets you delete files which are open, reclaiming the disk space when they're closed (or the process exits). On Win32 one cannot delete open files and Lucene must queue deletions.
So, yes, on Unix you may be searching index files that have been deleted. Whether such files exist or not is a matter for philosophers.
Doug
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