Broke -rootdir=dir when adding auto scan feature.
Broke -rootdir=dir when adding auto scan feature.

altMITgcm/MITgcm66h,altMITgcm/MITgcm66h,altMITgcm/MITgcm66h,altMITgcm/MITgcm66h,altMITgcm/MITgcm66h,altMITgcm/MITgcm66h,altMITgcm/MITgcm66h,altMITgcm/MITgcm66h