This document assumes you are building a traditional backend-heavy application as opposed to a frontend-heavy appliction which would typically use a framework like Angular or React. The use of these frameworks make this document irrelevant, however also require a change to your application architecture and a much larger overhead in order to get content onto a page, so as a simple way to build interactive web content a simple jquery based js stack will do fine.
It's important you use a directory structure which is impartial to your development environment, chosen server language (Python v. Java v. C# ...), and styling framwork (Twitter Bootstrap etc). This layer of separation means you can swap out the styles or the backend with minimal changes to the Js, simple and maintainable.
Here's an example from the project root:
