Merge pull request #525 from MG-RAST/develop

Various updates - see commit list.
Merge pull request #532 from MG-RAST/develop

Merge pull request #525 from MG-RAST/develop
Merge pull request #539 from MG-RAST/develop

Various updates.
Merge pull request #541 from paczian/master

fixed white eagle problem
Merge pull request #542 from MG-RAST/hotfix-3.10.1

Hotfix 3.10.1
Merge pull request #544 from paczian/master

heatmap color hotfix
Merge pull request #545 from MG-RAST/hotfix-3.3.11.2

Hotfix 3.3.11.2
Merge branch 'master' of github.com:MG-RAST/MG-RAST into hotfix-3.3.3.4
added all the user commands