Use npm-logical-tree to get a traversable dependency graph

Right now, we're doing a lot of this manually, and flattening the package-lock.json file. It'll save a lot (and likely protect against future breakage) to use this instead:

https://www.npmjs.com/package/npm-logical-tree

Start by reading the npm-logical-tree documentation and tracing the current manual flattening of package-lock.json in synp. Replace that approach with a traversable dependency graph, then verify that the converter still handles the package-lock.json and yarn.lock workflows without the existing manual dependency processing.

Written by the indexing model from the issue text.