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We have several PRs from 1.0 where we were not properly capturing local history. The CORE IResource operations for move/delete have an option for whether local history should be kept. We need to ensure we are using this option in the appropriate times. For example, "Replace With -> Base/Revision" should store the current resource into local history before replacing. Ensuring we are good local history citizens is a P1 plan item for 2.0.
Clarification, In the case of storing to local history prior to replace with base, specifically the case is if the local resource was modified/unreleased. If the user is replacing a resource for which we have an exact matching revision in the repository, the user could always get the state back from the repository history.
Fixed. We are calling IFile.setContents() with preserve history as true. Every CVS operation done within Eclipse works on IResources, we will benefit from any Eclipse history mechanism from now on. We are no longer bashing the file system then refreshing local.