nix-darwin-activation.nix

system.activationScripts.applications.text = let
  env = pkgs.buildEnv {
    name = "system-applications";
    paths = config.environment.systemPackages;
    pathsToLink = "/Applications";
  };
in
  pkgs.lib.mkForce ''
  # Set up applications.
  echo "setting up /Applications..." >&2
  rm -rf /Applications/Nix\ Apps
  mkdir -p /Applications/Nix\ Apps
  find ${env}/Applications -maxdepth 1 -type l -exec readlink '{}' + |
  while read -r src; do
    app_name=$(basename "$src")
    echo "copying $src" >&2
    ${pkgs.mkalias}/bin/mkalias "$src" "/Applications/Nix Apps/$app_name"
  done
      '';

{
description = "Example nix-darwin system flake";

inputs = {
nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
nix-darwin.url = "github:nix-darwin/nix-darwin/master";
nix-darwin.inputs.nixpkgs.follows = "nixpkgs";
};

outputs = inputs@{ self, nixpkgs, nix-darwin, ... }:
let
system = "aarch64-darwin";

  configuration = { config, pkgs, ... }:

    let
      env = pkgs.buildEnv {
        name = "system-applications";
        paths = config.environment.systemPackages;
        pathsToLink = "/Applications";
      };
    in {
      environment.systemPackages = with pkgs; [
        neovim
      ];

      system.activationScripts.applications.text = pkgs.lib.mkForce ''
        echo "setting up /Applications..." >&2
        rm -rf /Applications/Nix\ Apps
        mkdir -p /Applications/Nix\ Apps
        find ${env}/Applications -maxdepth 1 -type l -exec readlink '{}' + |
        while read -r src; do
          app_name=$(basename "$src")
          echo "copying $src" >&2
          ${pkgs.mkalias}/bin/mkalias "$src" "/Applications/Nix Apps/$app_name"
        done
      '';

      nix.settings.experimental-features = "nix-command flakes";

      system.configurationRevision = self.rev or self.dirtyRev or null;
      system.stateVersion = 6;
      nixpkgs.hostPlatform = system;
    };
in {
  darwinConfigurations."mini" = nix-darwin.lib.darwinSystem {
    inherit system;
    modules = [ configuration ];
  };
};

}

This is how I fixed it :)

for the latest nix version the function pkgs.buildEnv expects pathsToLink to be a list (like ["/A"]).

pathsToLink = ["/Applications"];

For the latest nix version you should wrap "/Applications" with [ ] in order to work and I think you should add system.applications.enable = true;. after system.activationScripts.applications.text = let , so Nix-darwin can manage macOS applications correctly.