Added script extract_barcodes.py, along with a tutorial. Partially addresses request in #531 regarding barcodes in headers.
Made changes suggested by Greg C.
fixes #1086
updated to create and use a top level rarefied table - fixing bug caught by @jrrideout
Made modifications to address problems/suggestions for code
Fixed conflict in Changelog.Md
made changes to remove consternation-causing passive voice.
Merge branch 'master' of github.com:qiime/qiime into issue-1086

Conflicts:
	qiime/workflow/core_diversity_analyses.py
fixed conflict in Changelog.md
Fix for conflict in tests/test_format.py
fixed dumb regex
fixed changed test to catch ValueError. Changed add_alpha_to_mapping to raise value error.
small syntax changes.
small changes
fixed error in formatting of help string
Merge pull request #1236 from walterst/extract_barcodes_nov_27_2013

Added script extract_barcodes.py, along with a tutorial. Partially addre...
Merge pull request #1289 from gregcaporaso/doc-fix

fixed error in formatting of help string
Merge pull request #1249 from gregcaporaso/issue-1086

fixes bug in core_diversity_analyses.py
removing old version of script docs
updated script docs