closed reference otu picking works in serial mode
added usearch_ref usage example
fixed test failure
modified so otu_table.biom is created in top-level output dir

previously was created under the otu picking output directory which was inconsistent with other upstream workflows, and annoying.
added note on new placement of otu_table.biom
fixed bug where params file could be ignored
Merge branch 'master' into issue-833
a semi-working version of parallel usearch_ref

this is giving intermittent failures, so still needs some work, but waiting on additional changes to the usearch code so won't fix now.
renaming workflows for clarity

partially addresses #708
added placeholder scripts to point users to rename scripts

partially addresses #708
noted renaming of scripts
fixed typo
Added application controller framework for usearch6.1 (open and closed reference OTU picking).  Modified usearch 5.X framework to work like uclust_ref for OTU matches and failures for future parallelization.
updated references to pick_otus_through_otu_table

these now refer to pick_de_novo_otus
renamed test data directories
updated references to pick_reference_otus_through_otu_table

now referred to as pick_closed_reference_otus
updated reference to pick_subsampled_reference_otus_through_otu_table

now refer to pick_open_reference_otus_through_otu_table.py
fixed typos
Merge branch 'master' into issue-833
Merge branch 'pick_otus_usearch_rev' of git://github.com/walterst/qiime into issue-833