get rid of unused .empty_directory files in the app generator

* public/stylesheets, test/functional, test/unit
these directories no longer exist

* test/fixtures, test/integration
these directories will be created through `empty_directory_with_keep_file` method
https://github.com/rails/rails/blob/f6bbc3f582bfc16da3acc152c702b04102fcab81/railties/lib/rails/generators/rails/app/app_generator.rb#L114

* app/mailers, app/models
these directories will be created through `keep_file` method
https://github.com/rails/rails/blob/f6bbc3f582bfc16da3acc152c702b04102fcab81/railties/lib/rails/generators/rails/app/app_generator.rb#L59