" a subset of a few files in the engine contains some code from other open source libraries"

The code that is ThreeJS derived includes most of the 3D engine classes including:

The main Renderer class (!). As well as the Texture, Camera, RenderTarget, ShaderLib, ShaderBuilder, EventTarget classes. Also the majority of the stuff in the /math, /lights, /pass directories.

GooEngine's renderer (not game engine) was clearly forked from ThreeJS some time ago and diverged (significantly in some places and for the better) but the lineage is clear.