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I haven't confirmed this, so I can't verify... but a user has noted that when he switches git branches (from a terminal), that Xamarin Studio loses the startup project state.
This could only happen when the userpref files are under source control or they get removed, and there would be nothing we could do about that.
Cannot seem to reproduce this in any other way. Marking the bug as NOT_REPRODUCIBLE until we get notified of this again.