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
Adding the possibility of creating stderr and stddev plots on the same run for run_alpha_rarefaction
Removed link to svn_documentation.

Fixes #830.
x_values are now scaled into range.

Still need to do some more testing.
Merge pull request #842 from jrrideout/issue-830

Removed link to svn_documentation.
Adding test for test_run_alpha_rarefaction_stderr_and_stddev
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