added --inputs and -i flags
added --inputs and -i flags

ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,squaresLab/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c