Merge pull request #436 from jfarid27/master

Added Limma Modal call. fixes #432.
Merge set manager updates with pull request #436
Added Limma Table. fixes #433.
Merge pull request #437 from jfarid27/working-branch

Added Limma Table. fixes #433.
Merge remote-tracking branch 'upstream/master'
Fixed scoping and resolvers #425

Solution basically is the inside out version of what it was before - now
instead of resolvers relying on injection for values, it's the other way
around the injection relies on resolvers.

Various cleanup associated with moving stuff around.

Added minimal code to launch embedded jetty during unit test, however
not running any tests at the moment.
Merge pull request #439 from lev-kuznetsov/master

Fixed scoping and resolvers #425
Merge remote-tracking branch 'upstream/master'
Added SelectionsController, log4j2
Added facet link from Set Manager to orefine
Added mev.css, Selection manager css.
Allow for annotation set updates in ORefine; add default color for new sets.
Merged pull request 434
Minor fixes for set manager accordion and previous merge of directive.js
Minor text edit
Minor fix: Set Manager accordion toggle
Set Manager accordions default to closed
Merge pull request #446 from apartensky/baylie-20131212-setmanager

Baylie 20131212 setmanager
Added Limma analysis download in tsv format. fixes #441.
Added Limma analysis significance note. fixes #448.