Only export bones that deform mesh geometry

Updates exporter to ignore bones that are not marked to deform the mesh.
Skin weight indices are mapped to included bone indices.

Addresses #49 

@repsac When I was reviewing your skin influence option addition, I noticed something was wrong and realized I had missed this change in the PR for three.js, so bone parent indices are currently wrong.
Not sure how I missed it, but updating this line resolves that issue .. sorry about that.