Merge pull request #391 from MG-RAST/develop

Version 3.3.6 update
Merge pull request #395 from MG-RAST/develop

Update to fix some of the broken job submissions lately and changes to new API (not being used yet)
Merge pull request #401 from MG-RAST/develop

Merging updates for hotfix
Merge pull request #404 from MG-RAST/develop

Updates to m5nr and fix for 'private' option missing from Analysis page.
first figure
add more examples
more examples
add abundance_matrix.pl
Merge pull request #408 from jaredbischof/develop

Edits to make API url's show up correctly in return structures and some fixes to API documentation.
add example
Merge branch 'develop' of github.com:MG-RAST/MG-RAST into develop
Merge pull request #410 from wgerlach/develop

api example scripts
Added two python examples
Merge branch 'develop' of http://github.com/MG-RAST/MG-RAST into develop
kevin created a directory for R based API examples
added scripts and placeholders for R based API examples
add couple simple r scripts
more comments for python example
Merge branch 'develop' of http://github.com/MG-RAST/MG-RAST into develop
provided downloadMGR in perl