Refactor add `config/application.rb` template

Source:
/railties/lib/rails/generators/rails/app/templates/config/application.rb
https://github.com/rails/rails @ 4-1-stable

This commit doesn't modify the generators behaviour.
Require YAML to use `config/secrets.yml`
Minor fix app secret_key_base in template: use secrets.yml

The Rails 4.1 `config/secrets.yml` is generated to store
the app secrets, let's use it!