updated to use open-reference otu picking and core_diversity_analyses.py

need to make an udpate to qiime to use change from #741.
updated to use open reference otu picking and core_diversity_analyses.py
added check_id_map.py step
Merge branch 'make_bipartite_network.py' of git://github.com/wdwvt1/qiime
Merge branch 'master' into illumina-tutorial-updates

Conflicts:
	examples/ipynb/illumina_overview_tutorial.ipynb
more updates to the tutorial following re-organization of data in the tutorial tgz
fixed typos
Merge branch 'master' of git://github.com/qiime/qiime
updated to fix some bugs in the commands
removed output from each command
includes output for a full successful run
Merge branch 'master' of git://github.com/qiime/qiime
Modified pycogent_backports/usearch.py to correctly pass HALT_EXEC for usearch_qf (5.X) code.  Also fixed typo in scripts/pick_otus.py
Add check where all samples are filtered out

Add a test to the test suite with this case.
Add try except block for --valid_states input

Fixes #779
Fixes issue #903, now checks for metadata column if mapping file provided
summarize_taxa.py provides an informative error message on no observation metadata

this fixes #219
fix issue 705 by moving where consensus tree is placed
Clarified error message.
Modified check_id_map.py to 1.  allow suppression of html generation and 2.  add warnings for empty fields before the Description column