Documenting my System

Hey everyone! Here's a question for my favorite Hashnoders: I have been working on a complex system for quite a while, but my documentation has always been lacking. Very so. Let me be honest. There is no real documentation :(

So how should I document my creation? Basically it's an application host written in JS for Node.JS. I need to write tutorials on how to set it up and use it. Additionally I have to write references for all the modules and global sandbox objects.

In the past I used Doxygen, but it is not easy to use with dynamic JS and looks dated (ugly, to be frank). I really like the style of the unofficial Vulkan tutorial and I considered using the Daux.io, or at least build something which looks similar. What do you think? Have you made any good experiences? What kind of docs style do you prefer?