Compare alpha div improvement

This commit alters compare_alpha_diversity.py so that it outputs the average alpha diversity of the groups being compared. I had to modify workflow/core_diversity_analysis.py because it depended on the output formatting of compare_alpha_diversity.py. I have verified that the command for core_diversity_analysis.py works correctly but I think @gregcaporaso should take a look to make sure this doesn't alter something I have overlooked or otherwise has been unaccounted for.