(sandbox/tacc) Another merging of trunk to get the recent changes

src/Makefile

src/base/kaldi-math.h

src/bin/compute-wer.cc

src/doc/README

src/doc/io.dox

src/doc/io_tut.dox

src/doc/tutorial_running.dox

src/feat/pitch-functions-test.cc

src/feat/pitch-functions.cc

src/featbin/paste-feats.cc

src/fstext/Makefile

src/fstext/epsilon-property-inl.h

src/fstext/epsilon-property-test.cc

src/fstext/epsilon-property.h

src/fstext/fstext-utils-inl.h

src/fstext/fstext-utils.h

src/gmmbin/gmm-est.cc

src/hmm/transition-model.h

src/ivectorbin/ivector-extractor-acc-stats.cc

src/kwsbin/generate-proxy-keywords.cc