fix Nix build and add updater

- move unnecessary toplevel files to nix/
- added patch that ignores the submodule (revert)
- add update script run by a workflow

.github/workflows/nix-update.yaml

@@ -19,7 +19,7 @@ jobs:
           auto-optimise-store = true
           experimental-features = nix-command flakes
     - name: Update lockfile
-      run: nix flake update
+      run: nix/update-inputs.sh
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         commit_message: "[gha] bump flake inputs"