Updated text for list description
Seperated shell scripts and functionality

Scripts were split and command line functions were put in the scripts
directory. The functions behind the shells were moved to the american
gut site, and names were changed slightly.
Merge branch 'master' of https://github.com/qiime/American-Gut into module2_modularization

Conflicts:
	scripts/generate_otu_signifigance_tables_AGP.py
Test Code for Make Phyla Plots!
Added unclassified description above the famoly level
Merge pull request #25 from JWDebelius/module2_modularization

Module2 modularization