Added a SourceTracker tutorial rst file and image related to that tutorial
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
Merge branch 'master' of github.com:qiime/qiime into sourcetracker_tutorial
Removed example output from help command in order to avoid confilicts with changes to the option list in future releases.
added text to clarify the description of the filter_otus_from_otu_table.py
Improved the description of adding columns to the mapping file.
made a few minor changes to clarify descriptions and fix grammer.
added the print_qiime_config.py command to the tutorial.
Fixing option types and example definition
Fixing --metrics option type for beta_diversity.py
Fixing scaling_method and vectors_algorithm option types for make_3d_plots.py
Fixing metrics option type of parallel_alpha_diversity.py
Merge branch 'master' of github.com:qiime/qiime into par_alpha_div
Fixing the way params is passed in parallel_alpha_diversity.py
Merge branch 'master' of github.com:qiime/qiime into make_3d_plots
Adding eldeveloper's comments
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.