Indirect package set flake input

[brynblack]

Description

This PR incorporates the new indirect flake input system.

Tasks

• [x] 1. Update flake.nix to use indirect inputs

Final checklist

• [x] Domain specific tests
• [x] Full tests
• [x] Updated inline-comment documentation
• [x] Lint fixed
• [x] Squash and rebased
• [x] Sanity check the final build

[brynblack]

Going to merge this, to test if new CI image works with indirect inputs.