Move Flatpak management to system configuration

Flatpak management has been refactored from Home Manager and nix-flatpak to a new system/flatpak.nix module, now imported in system/common.nix. This centralizes Flatpak enablement and declarative app management at the system level, simplifying configuration and maintenance.

system/common.nix

@@ -1,6 +1,10 @@
 { config, pkgs, ... }:
 
 {
+  imports = [
+    ./flatpak.nix
+  ];
+
   # Common system configuration shared across all machines
   
   # Bootloader
@@ -10,9 +14,6 @@
   # Networking
   networking.networkmanager.enable = true;
 
-  # Enable Flatpak
-  services.flatpak.enable = true;
-
   # Timezone and locale
   time.timeZone = "Europe/London";
   i18n.defaultLocale = "en_US.UTF-8";

system/flatpak.nix

@@ -0,0 +1,47 @@
+{ config, pkgs, ... }:
+
+let
+  grep = pkgs.gnugrep;
+  
+  # Declare the Flatpaks you want on your system
+  desiredFlatpaks = [
+    "io.github.zen_browser.zen"
+    # Add more Flatpak apps here
+    # "com.spotify.Client"
+    # "com.discordapp.Discord"
+  ];
+in {
+  # Enable Flatpak
+  services.flatpak.enable = true;
+  
+  system.userActivationScripts.flatpakManagement = {
+    text = ''
+      # Ensure the Flathub repo is added
+      ${pkgs.flatpak}/bin/flatpak remote-add --if-not-exists flathub \
+        https://flathub.org/repo/flathub.flatpakrepo
+
+      # Get currently installed Flatpaks
+      installedFlatpaks=$(${pkgs.flatpak}/bin/flatpak list --app --columns=application)
+
+      # Remove any Flatpaks that are NOT in the desired list
+      for installed in $installedFlatpaks; do
+        if ! echo ${toString desiredFlatpaks} | ${grep}/bin/grep -q $installed; then
+          echo "Removing $installed because it's not in the desiredFlatpaks list."
+          ${pkgs.flatpak}/bin/flatpak uninstall -y --noninteractive $installed
+        fi
+      done
+
+      # Install or re-install the Flatpaks you DO want
+      for app in ${toString desiredFlatpaks}; do
+        echo "Ensuring $app is installed."
+        ${pkgs.flatpak}/bin/flatpak install -y flathub $app
+      done
+
+      # Remove unused Flatpaks
+      ${pkgs.flatpak}/bin/flatpak uninstall --unused -y
+
+      # Update all installed Flatpaks
+      ${pkgs.flatpak}/bin/flatpak update -y
+    '';
+  };
+}