Commuter rail riders later this year will be able to purchase and display tickets on their smartphones instead of fumbling with cash or fishing for prepaid paper tickets and passes, under an agreement signed Friday by the MBTA. With an estimated two-thirds of riders carrying smartphones, the application could also make fare collection more efficient on crowded trains and reduce on-board cash transactions for the MBTA. The T would be the first major US commuter rail to offer passengers an alternative to paper.