chore: Organize flake

[eureka-cpu]

Motivation

Just getting familiar with the code base. I see that the flake has a lot going on, and there's a good number of anti-patterns so this is really just a cleanup PR.

Solution

Use writeShellApplication instead of custom wrapper type mkTask. mkTask is essentially trying to do what writeShellApplication already does, without the added benefit of running shellcheck.

Organize derivations and overlays for better composability, and less likelihood of getting or incorrectly setting policy decisions used by downstream consumers.

Add legacyPackages and apps for package introspection from the repl and discoverability.

Add the default package to checks for convenience.

Checks

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• made this PR as small as possible
• unit-tested any new functionality
• linked any relevant issues or PRs
• included screenshots (if this involves a front-end change)

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[eureka-cpu]

If mkTask is used a lot downstream, to avoid breaking things we could change the function such that the inputs stay the same, but the actual returned value is writeShellApplication and using it prints a deprecation warning. That would make it a bit easier to eventually adopt the right pattern.