ctc: various reorganizations and fixes; adding some test code for nnet-ctc supervision (unfinished); adding some documentation

CTC code: Add testing code for context-dependent CTC (CCTC) transition-model object, and numerous bug fixes

Adding language modeling code (and test code for it) that is to be used as a phone language model in CTC modeling.

Adding script to generate lattices with alternative pronunciations of training utterances (to be used in CTC)

added max-change related stats in NaturalGradientAffineComponent

Fixing bug in ivector/logistic-regression-test.cc

Modified virtual functions Scale and Add 

Fixing bug in ivector/logistic-regression-test.cc and removing trailing whitespace from other logistic regression files

Adding nnet2 function NnetComputationChunked

Added --scale option to nnet3-am-copy, useful for shrinkage of parame…

nnet3 lstm train script bug fix

add log-prob-per-frame in nnet3 training log