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Tidy, update, and document Crystal Toolkit scene generation code #703

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mkhorton
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There are a few new features in Crystal Toolkit I'd like to implement, but I noticed the corresponding JavaScript code hadn't been updated in a while and thought some early spring cleaning might help :)

Creating this PR in draft until it's ready to merge, but includes:

  • Updating three.js from 0.139 to 0.160
  • Updating parcel (build tool) and some small updates to make sure code still builds with latest version
  • Remove ColladaExporter, deprecated in favor of GLTF/GLB which are actively maintained and more recent standards
  • Types and documents SceneSettings to make it easier to see what is configurable
  • Adding docstrings to key functions
  • Renaming/moving some files for better organization
  • Fix bug related to GLB export
  • Fix bug related to objectJson.origin

Removal of `ColladaExporter` (deprecated in favor of GLTF/GLB, which are the latest industry standards). All geometries are now `BufferGeometry` by default, so constructors have been renamed.
@yang-ruoxi
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this is awesome @mkhorton thanks for the PR. Let me know if you want to coordinate on some parts?

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