Deprecate `check_manifest.py` (in favor of recreate+`diff`)

[tcompa]

In the GitHub CI, we rely on check_manifest.py.

We should rather proceed as in https://github.com/fractal-analytics-platform/fractal-tasks-template/blob/main/project/.github/workflows/build_and_test.yml.jinja:

      - name: Regenerate the manifest
        run: python src/{{package_name}}/dev/create_manifest.py

      - name: Check if manifest has changed
        run: |
          if [ -n "$(git diff --exit-code ./src/{{package_name}}/__FRACTAL_MANIFEST__.json)" ]; then
          echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/{{package_name}}/dev/create_manifest.py' and commit the changes."
            exit 1
          else
            echo "__FRACTAL_MANIFEST__.json has not changed."
          fi

This is required, because create_manifest.py is aware of a more structured set of inputs (e.g. #874), which cannot be inferred from the manifest alone. This means that we cannot check the self-consistency of the manifest without recreating it.