converted to rails 4.1.2 project
added files that came with initialization of the project as 4.1.2
added first Test for the RaxmlCotroller
updated some Gems in the Gemfile
corrected Raxml.collectCites which had a wrong character in the string
use of new "Rails.root" instead of ENV["RAILS_ROOT"]
reformatted db.migrate files so that the fields are easier to read
replaced :name => with name: syntax in several places
Merge branch 'master' of https://github.com/nwoetzel/EPA-WebServer