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In org.eclipse.team.core.variants.ResourceVariantTreeSubscriber.members(IResource) there is an iteration over all members of a resource which was passed as an argument for this method. It is performed to remove deletion conflicts and unsupervised resources from members list. I have found an incorrect condition: if (!isSupervised(resource)) In result, if resource is not supervised all its members will be removed. It should be: if (!isSupervised(member)).
Created attachment 185214 [details] fix
Fixed in HEAD, available in builds >=N20101215-2000. Thanks Wojtek.
The change is tagged with I20101221-0800 (and with tags that came later). Verified by code inspection in I20110124-1800.