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Here you go: https://github.com/atom/atom-shell/blob/master/docs/developm...

THREE.js... is that related to node-webkit, or it's just what you're using to do unrelated 3D stuff? (are you using three.js to draw window chrome, for example)

It's for unrelated 3D stuff :) node-webkit is just there as our desktop shell.

afaik, node-webkit has some features that Atom Shell doesn't like window transparency, but because node-webkit heavily patches Chromium itself, it typically lags further behind in Chrome (Atom Shell is currently at Chrome 39, whereas node-webkit just hit 38, and was previously stuck at Chrome 30).