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It would be good to mark Tree deprecated for 0.9 and remove it before 1.0... or simply remove it for 0.9...
http://egit.eclipse.org/r/1077 marks these as deprecated. Not sure we can kill all of them during the 0.9 development cycle, but I would like to get rid of them all before 1.0.
Fixed by I2b28f9cddc36482e1ad42d53e86e9d6461ba3bfc