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I use flakes and all hosts are configured from a single flake, where each host has its own configuration. I have some custom modules and even custom package in the same flake. I also use home manager. I have 4 hosts managed in total: home server, laptop, gaming PC, and a cloud server. All hosts were provisioned using nixos-anywhere + disko, except for the first one which was installed manually. For secrets I use sops-nix, encrypted secrets are stored in the same flake/repo.

NixOS

There's a plug to enable folder based sidebar navigation https://github.com/joekrill/silverbullet-treeview