Migrate away from overlays

Historically, overlays have been the mechanism for extending the package sets from some Nix code. However in the flake world these don't make as much sense. In a version 2 of FIRE, we should attempt to move away from overlays as the internal extension mechanism and prefer exported scopes, perhaps as a module for flake-parts.

For more reasons why: https://zimbatm.com/notes/1000-instances-of-nixpkgs