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In bug 356477, I requested a new server API for staging a selection of file. We need a quite similar way to do bulk un-stage as well.
I reckon it has been already fixed in bug 338202, see the last comment there (bug 338202, comment 5) and http://wiki.eclipse.org/Orion/Server_API/Git_API#Unstaging_a_group_of_files (just added). Of course, you are free to reopen this bug if you don't think that the current approach is not an acceptable solution for you. *** This bug has been marked as a duplicate of bug 338202 ***