An automatic document feeder includes: an inlet; an outlet; a transfer system configured to transfer a document from the inlet to the outlet; an input transfer path configured to guide a document during transfer from the inlet passed a scanning point to an end point positioned above the inlet; an output transfer path configured to guide the document during transfer from the end point passed the scanning point to the outlet; a secondary system configured to feed the document from the inlet; and a drive system configured to drive the transfer elements and the secondary system, wherein the drive system controls the transfer system such that, in at least some instances, operation of the secondary system is independent of operation of the transfer system.