changed {} to None as default function parameters and more

It is advised not to use mutable object (such as {} and []) as default
parameters to avoid possible bugs. See
http://satyajit.ranjeev.in/2012/01/12/python--dangerous-default-value-as-argument.html
for details.

Also fixed a typo
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
Add descriptive error to add_alpha_to_mapping_file

The library function was changed to check for the existance of the
specified rarefaction depth; it will now raise an exception if a
non-existant depth is passed. This exception is now catched from the
script interface and displayed using option_parser.error.

The test suite was updated accordingly for this module.

An unnecessary type cast was also removed from the script interface.

This should fix #827
Add available depths to the exception message
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