beginning to add cli support for xml in train/predict/evaluate (not done)
UMLS and GENIA should default to off
Outptuting debug info
Merge branch 'master' of https://github.com/mitmedg/CliCon into command-line-interface

Conflicts:
	clicon/train.py
syncing up with master
syncing up with master
Clean up user output
CLI functionality for train/predict
Make coherent pipeline status updates for user
modified Note::write_i2b2() so it does not write directly to a file
Merge branch 'command-line-interface', remote-tracking branch 'origin'