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Looks promising. Just out of interest, do you think it would be easy to build a hardware accelerated 2D interface using this setup?
Have you looked at pixi.js?

http://pixijs.com

I wasn't aware of pixi.js before, but I am now, I think it's great, thank you atrilumen! This was probably my favourite project using it... www.spaceneedle.com/home/
Looks like it will be useful. I often make small visualisations of my work in physics with Three.js and the boilerplate time gets annoying sometimes.
Very nice. Especially good job on making a nice page detailing how everything works.

You might be interested in a similar boilerplate that I put together, which using Require.js to structure the application: https://github.com/felixpalmer/amd-three.js

One pain point that my setup solves that I haven't seen many THREE.js boilerplates tackle is the ease of writing GLSL for creating custom shaders. Here I've supplied a Require.js plugin which allows you to pull your GLSL code in as dependancies and provides some basic pre-processing like #import and modifying #defines from JavaScript.

thanks! I'll see how you fixed the problem and try to add it to the boilerplate
Very cool, I'll be keeping this in mind for the next Ludum Dare! :)