Modify generated flake.nix to match holonix default template

[mattyg]

It might be good for nix flake generated by scaffolding to mostly match the holonix default template. This lets us be consistent in any documentation that has to explain to app devs how to update their flake (i.e. in upgrade guides). It also makes it clear to app devs how they can remove unused holochain packages from their flake.

Holonix default template: https://github.com/holochain/holonix/blob/main/templates/default/flake.nix (not using inputsFrom, but specifying each included package from holonix)

Scaffolding nix flake: https://github.com/holochain/scaffolding/blob/main-0.4/src/scaffold/app/nix.rs (using inputsFrom)

[ThetaSinner]

This didn't get done because of a complaint about the ability to use inputsFrom with the new Holonix flake.