Upgrade configs

As rails 4 is already running, we can upgrade some of our configs to look more likely a modern app.
2 things in this:
 - using `Gemcutter::Application` is not a thing, should use `Rails.application` instead.
 - use secrets.yml instead of secret_token.rb init (http://guides.rubyonrails.org/upgrading_ruby_on_rails.html#config-secrets-yml)