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Currently, the command can only be executed on a repository level. It would be helpful to be able to reset a single file, an equivalent of "git reset {ref} -- {path}".
[1] is a first step in this direction and will allow to replace files in the working tree from HEAD [1] http://egit.eclipse.org/r/#change,2415
reset with paths rfc http://egit.eclipse.org/r/#change,3453
Fixed with 37fe0988b26b7893888a073a33ccf0865723ca8b.