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Bug 334112 and the related patch addresses what should happen to the index when a project is moved. There is however no way to commit using the information in the index in the current commit dialog. The dialog fail to do this. In particular it cannot se the project at the old location and will only see the project in the new location. Hence even if Bug 334112 is fixed, and EGit(only) user will not be helped much.
I think this should be solved with the ability to commit non workspace changes, right?
I think this was fixed in the meantime, otherwise please reopen.