refactor/clean-up-codebase

[djacu]

Removes unused functions from flake.nix. Much of the functionality happened in let in blocks and was extracted into functions that can be called. Libraries were created so functions can be organized. Functions were documented with examples. The library has been exposed as a flake output for easy development and debugging.

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[GTrunSec]

No special critical here, looks good so far.

I'm going to talk about some motivation for the refactorV2 at another issue.