More work on s5 scripts; add comments in fmpe.cc

egs/wsj/s5/run.sh

egs/wsj/s5/steps/align_si.sh

egs/wsj/s5/steps/decode_fmllr.sh

egs/wsj/s5/steps/decode_fmmi.sh

egs/wsj/s5/steps/decode_si_fromlats.sh

egs/wsj/s5/steps/make_denlats.sh

egs/wsj/s5/steps/train_deltas.sh

egs/wsj/s5/steps/train_lda_mllt.sh

egs/wsj/s5/steps/train_mmi.sh

egs/wsj/s5/steps/train_mmi_fmmi.sh

egs/wsj/s5/steps/train_mono.sh

egs/wsj/s5/steps/train_sat.sh

egs/wsj/s5/utils/split_scp.pl

egs/wsj/s5/utils/summarize_warnings.pl

src/transform/fmpe.cc