Upgrade arahy to rails 3.2

* Added assets
* Added config settings
* Removed deprecation warning
* Upgraded specs and gems
Cleaned JavaScript.
Enabled pushed upgrade to species.

* Enabled asset pipeline
* Updated gems
Upgraded to Rails 3.2.12.

* Added application-jquery.js
Pushed Rails 3.2.12 to all species.
Added HTTP <-> HTTPS redirects.

* Cleaned up code.
* Updated specs.
Push HTTP <-> HTTPS redirects to all species.
Upgrade to Rails 3.2.13
Updated species for HTTPS <-> HTTP

* Added protocol to navigation
* Added secure session storage for production
* Moved jQuery to public/javascripts
Refactored protocol detection and updated urls.yml
Updated cas urls for production.
Updated HTTP error pages for asset pipeline.