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I moved most of my user logic into home-manager, you can see my flakified home-manager settings here: https://github.com/jonringer/nixpkgs-config
You can use flakes and home-manager. If you want an example of how to structure/setup your configuration you can check mine EdenEast/nyx. My configuration defines my nixos machines, darwin machines, and generic home-manager output (used for things like wsl).
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.