Here is how i like to do it. 

js
  thirdparty
    jquery
    jquery-ui
  app
    view
      view1.js
      view2.js
    presenter
      presenter1.js
      presenter2.js
    model
      model1.js
      model2.js
    templates
      template1.html
      template2.html
    utils
      utils.js

css
  thirdparty
     jqueryui.css
  myapp.css
  mymodule.css


I have a build process that packages the code for production. 

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