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Instead of the obscure "Problem deleting resource" when trying to refresh a project from CVS (if something in the filesystem has changed but Eclipse hasn't noticed), why not just force the refresh and perform the replacement?
Created attachment 50527 [details] screenshot of unhelpful error message
... or at the very least, change the message to be "cannot update resource: [...]. Please refresh and try again."
*** This bug has been marked as a duplicate of 35355 ***