$ mkdir app/assets/javascripts/application
$ mkdir app/assets/javascripts/application_head
copy stuff you want in the head into the application_head directory and the rest into application
app/assets/javascripts/application_head.js:
//= require_self
//= require_tree ./application_head
app/assets/javascripts/application.js:
//= require_self
//= require_tree ./application
in config/application.rb, add
config.assets.precompile << 'application_head.js'