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[wtp-dev] WTP is removing temporary folders on every publish

Hi.
I'm using Eclipse Galileo, and have a web project under a Tomcat 6 server using Lucene for full-text indexing.
Lucene creates the indexes in a folder under the project deploy path.
However, every time I save a file in eclipse, the server publish is removing the index folder, which is a pain, as it renders the application unusable, and I have to stop, start so indexes are recreated (which also takes a long time, depending on data).
Is there a way to make WTP not removing folders which are not in the workspace?
Thanks.
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Luis Fernando Planella Gonzalez