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https://issues.apache.org/jira/browse/LUCENE-458?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Michael Busch resolved LUCENE-458.
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    Resolution: Duplicate

The problem here apparently is that when the JVM crashed not all files are 
properly synced with the FS.
This seems to be a similar problem to LUCENE-1044. 

> Merging may create duplicates if the JVM crashes half way through
> -----------------------------------------------------------------
>
>                 Key: LUCENE-458
>                 URL: https://issues.apache.org/jira/browse/LUCENE-458
>             Project: Lucene - Java
>          Issue Type: Bug
>    Affects Versions: 1.4
>         Environment: Windows XP SP2, JDK 1.5.0_04 (crash occurred in this 
> version.  We've updated to 1.5.0_05 since, but discovered this issue with an 
> older text index since.)
>            Reporter: Trejkaz
>
> In the past, our indexing process crashed due to a Hotspot compiler bug on 
> SMP systems (although it could happen with any bad native code.)  Everything 
> picked up and appeared to work, but now that it's a month later I've 
> discovered an oddity in the text index.
> We have two documents which are identical in the text index.  I know we only 
> stored it once for two reasons.  First, we store the MD5 of every document 
> into the hash and the MD5s were the same.  Second, we store a GUID into each 
> document which is generated uniquely for each document.  The GUID and the MD5 
> hash on these two documents, as well as all other fields, is exactly the same.
> My conclusion is that a merge was occurring at the point the JVM crashed, 
> which is consistent with the time the process crashed.  Is it possible that 
> Lucene did the copy of this document to the new location, and didn't get to 
> delete the original?
> If so, I guess this issue should be prevented somehow.

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