ci: delete empty submodules file

Created by: jhchabran

The empty .gitmodules file triggered the Buildkite submodules command during the checkout phase. As this file was empty this caused an error which lead to always displaying a warning sign and always expanded the "Preparing working directory".

Before:

After

---

This has been driving me nuts since I've started looking at those build logs ⚠️🧹😤