Improve the deps tool (niv fork) and the Nix dependency pinning infrastructure. Goals: 1. Add auto-override field to control which sources override nixpkgs packages 2. Fix version field inconsistency (version vs rev confusion) 3. Improve documentation with decision tree and workflow examples
Context: deps is a fork of unmaintained niv. The system uses Sources.json for pins, Sources.nix for fetching, and overlays in Deps.nix/Python.nix/Haskell.nix to apply them.