Restore permissions in nixpkgs

scripts/Common/OS/setup.fish

@@ -65,6 +65,7 @@ function runSetup
             set -l path "$mountDir/$nixPkgsDir"
             and mkdir -p (dirname "$path")
             and cp -r "$nixPkgsDir" "$path"
+            and git -C "$path" reset --hard
         end
 
         and runHook initOS "Please set up a function `initOS` for initializing the mounted OS and installing valhalla dependencies"