Remove the file from filesystem

rm content/testing-your-dkim-and-spf-setup/index.md

Remove it from git tracking

git rm content/testing-your-dkim-and-spf-setup/index.md

Commit the change

git commit -m “Remove duplicate index.md from wrong location”

Restore missing files

git checkout content/testing-your-dkim-and-spf-setup/index.md git submodule update –init –recursive