fixes #1086
updated to create and use a top level rarefied table - fixing bug caught by @jrrideout
Merge branch 'master' of github.com:qiime/qiime into issue-1086

Conflicts:
	qiime/workflow/core_diversity_analyses.py
fixed dumb regex
Merge pull request #1249 from gregcaporaso/issue-1086

fixes bug in core_diversity_analyses.py