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Setup SDK - 4.3.0.I20130205-0800 EGit - 2.3.0.201302060400-rc1 When I delete a project from the workspace and chose the option to delete the files from the file system, the deleted files are not shown in the "git staging" view. If I use git on the cli, the files appropriately appear as deleted.
This is a refresh bug. If you press the refresh button in the staging view the deleted files appear, though one would expect this to happen automatically. My guess is that this is because we now optimize the refresh by listening to resource change events that does not happen when whole projects are deleted.