Fixed https://github.com/NICTA/scoobi/issues/308: MR job numbering broken in HadoopMode for job plans with more than 1 layer

Fixed by computing, at each layer, the total number
of MSCRs in all previous layers, and plumbing that
down to configureMscr, where the "Step X of Y"
gets configured.
Fixed https://github.com/NICTA/scoobi/issues/306: In-memory mode does not keep track of hadoop counters