nltk dependency commented and main.py script tested.

Everything seems to work. Dump files look good.
Compared to legacy versions, some small details have changed like file
paths. Check main.py for changes.

15:09 - snape@moo:src $ python main.py
~/Documents/bazaar/data/brontosaurus expe_211013 True True False
------------------------------------------------------------------------
--------
Reading folder:
/Users/snape/Documents/bazaar/data/brontosaurus/expe_211013/data
Writing folder:
/Users/snape/Documents/bazaar/data/brontosaurus/expe_211013/dumps
Expects a blacklist: True
Expects an ontology: True
Expects a flat resource: False
------------------------------------------------------------------------
--------
FIRST
------------------------------------------------------------------------
--------
Reading lemma
5440 lemma read.

Reading blacklist
Blacklist content: index, plant, level, number, content, amount, time,
size

------------------------------------------------------------------------
--------
LEARNING ONTO
------------------------------------------------------------------------
--------
Reading onto
446 terms currently in memory.

The following inconsistencies were found in the ontology:
'None' none of its ancestors are typed '()'

Reading onto heads
446 terms currently in memory.

The following inconsistencies were found in the ontology:
'None' none of its ancestors are typed '()'

Saving after learning onto
------------------------------------------------------------------------
--------
TAGGING
------------------------------------------------------------------------
--------
Tagging heads
200 terms tagged.

Saving after tagging
------------------------------------------------------------------------
--------
Done!
------------------------------------------------------------------------
--------
Merge remote-tracking branch 'origin/BioNLP2013' into cleanup

The cleanup is finished thus it replaces the BioNLP2013 branch.