prototype-rails provides Prototype, Scriptaculous, and RJS for Rails 3.1.
Prototype and Scriptaculous are provided via the asset pipeline and you do not need to copy their files into your application. Rails will get them from prototype-rails automatically.
You may want to add them to your app/assets/javascripts/application.js:
//= require prototype
//= require prototype_ujs
//= require effects
//= require dragdrop
//= require controls
New applications using this may also want to add
config.action_view.debug_rjs = true
to their config/environments/development.rb.