Fix bug causing LargeD0 job options to ignore efficiency histograms

LargeD0 job options were missing the efficiency histograms, this commit fixes that.
In addition, several  (but not all) requests to delete instead of comment out lines
were commented by the L1 MR shifter and have been incorporated in this update.
I have also attempted to delete the cmt folder...


Former-commit-id: 1e754066