Clean up README

While style argueably is mostly a matter of taste, this change aims to

  * make it easier to jump to searched paragraphs by reducing and 
    consolidating heading levels
  * group similar information together
  * make copy and paste of command line examples easier

Have a look at https://github.com/protobuf-ruby/beefcake/blob/simplify-readme/README.md

@matttproud