flake.nix is too big

[steve-chavez]

Problem

It's hard to navigate flake.nix since it contains many scripts.

Solution

Modularize the scripts into different folders.

This should be done after #1563, to identify potential deduplication first.

[samrose]

@steve-chavez I think we could deduplicate without the need to first inline everything.

[samrose]

resolved with #1681