Great tutorial I found on GitHub: JavaScript Stack from Scratch
This is a minimalistic and straight-to-the-point guide to assembling a JavaScript stack. It requires some general programming knowledge, and JavaScript basics. It focuses on wiring tools together and giving you the simplest possible example for each tool. You can see this tutorial as a way to write your own boilerplate from scratch.
You don't need to use this entire stack if you build a simple web page with a few JS interactions of course (a combination of Browserify/Webpack + Babel + jQuery is enough to be able to write ES6 code in different files with CLI compilation), but if you want to build a web app that scales, and need help setting things up, this tutorial will work great for you.
Certainly worth the time…