Node versioning and package management system

Create an overrides/versioning system that lets users override document nodes (subgraphs), either overriding part of the subgraph or creating a copy of the full document node; then make a way of tracking versions and upgrading old documents to new versions

The issue does not name files, tests, or entry points. Start by locating the document-node and subgraph representations, then trace how documents are serialized and loaded. Done would require a defined override model, version tracking, and an upgrade path for older documents, but the issue does not specify their expected behavior.

Written by the indexing model from the issue text.