Merge branch 'fix_issue_685' of https://github.com/antgonza/qiime into fix_issue_685
Modified compare_alpha_diversity.py

This commit modifies compare_alpha_diversity.py so that it will output the average alpha diversity of the compared categories. I find myself wanting this information frequently when doing tests and it wasn't available. These changes modify the output of the script so that you pass a directory to be created and it puts two files in that directory. One specifying the comparisons and their values, and one specifying the averages and std's of the averages for each treatment group. I have updated the script usage tests and verified that they work so that jenkins should be happy.

In addition, I needed to modify core_diversity_analysis.py because it depended on the output. I only had to modify several lines in the workflow/core_diversity_analysis.py code to alter the way it was handling the output directories.
Removed old test files which have been migrated.
Modified tests

Tests now use assertFloatEqual where appropriate which will hopefully resolve the failures with the latest jenkins build for compare_alpha_diversity.py. Also changed some locations in test_workflow/test_core_diversity_analysis.py to reflect changes in output structure of compare_alpha_diversity.py
Modifies test_downstream.py to account for alpha div changes.
Modifies to address comments.
Forgot a documentation change.
Modified documentation in script and Changelog.md
Commiting modified test_downstream.py

Avoids automerge conflict resulting from simultaneous edits.
Merge branch 'master' of https://github.com/qiime/qiime into compare_alpha_div_improvement

Conflicts:
	tests/test_workflow/test_downstream.py
set suppress warnings flag to True by default so that warnings are not printed
first pass at adding missing text
various clean-ups to text and formatting
updated order of tutorials
updating to reflect that subsampled should always be used
clean-ups to text. Fixes #851
updated some text
added template document
Merge branch 'OTUcat' of git://github.com/clozupone/qiime into clozupone-OTUcat
added several sections