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org.openide.filesystems.Repository.{add|remove}FileSystem are deprecated and there is no reason to create temporary filesystem, add it for a while to repository and remove it during deployment process in j2eeserver module.
Radim, thanks for finding this. Still, pretty bad bug report: What are the consequences for the user? What is the justification of the P2 priority?
Personally I do not care about priority. Currently it is not expected that any module will alter repository content.
Fixed in ServerFileDistributor and InitialServerFileDistributor.
thanks, I've seen this was commited to trunk (4.0 and to promoe_dev branch)