Add emperor configuration file

This configuration file supports an installation of Emperor only. This
should be useful to deploy in the Jenkins-CI server.
Remove the setup tools
Change directory name
Merge pull request #82 from jrrideout/master

Remove extraneous README.md files
Merge pull request #83 from jrrideout/master

Add setuptools target to biom-format conf
Add setuptools to the configuration file
Merge pull request #81 from ElDeveloper/emperor_conf

Add emperor configuration file
Update for biom-format 1.3.1, 1.3.1-dev

Also update QIIME to use biom-format 1.3.1.
Merge pull request #84 from jrrideout/biom-1.3.1

**NOT READY FOR MERGE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!1** Update for biom-format 1.3.1, 1.3.1-dev