Start a package.json for vanilla node dependencies

Continuing where #1772 started, I've been able to identify 4 node packages that are vendored and can thus be declared in a package.json. The rest are either forked or not used. I've updated doc/for-committers.md with more details.
@ibdknox I've noticed the following node dependencies are not used - bencode, harbor, jshint, marked, source-map, walkdir, watchr, acorn.js . Actually on the atom-shell, I saw bencode [was modified](https://github.com/LightTable/LightTable/commit/d951744c5832e444d782f777f001d8377a07cab0) but it's not used, right? Any objections to removing these on this pull?