We use static/js/base.js as a single point of entry. Within this file, we lazy load additional elements using require.js.
In addition, we use Cl as global namespace for all our custom code or addons to keep the global namespace clean. Following this guideline, we use as initiation Cl.Base or Cl.Application for our website. See static/js/addons/cl.utils.js as example.
Always add the appropriate prefix to the filename. If there are multiple libraries used within the file, the wrapping namespace should win. In case of Cl.Utils we use jQuery, MBP and class.js. Cl wins as Cl.Utils is the wrapper.
Separate modules which are plug-n-play able and add them into this folder. Traditionally the classjs-plugins are added here.
If you use external addons, such as jquery.select2, ensure that those files get added minified. Try to avoid changing the code of external addons as this over complicates the update process if hotfixes are released.
class.js is simpler than the bloated jQuery UI and offers faster performance. It simply provides a more traditional class based inheritance model but still uses prototypal inheritance.
Additional libraries such as respond.js or html5.js provide html/css shivs for older browsers.