Nested Git repositories can appear as phantom submodules

Tonight I helped a student who was trying to publish a project to GitHub with Android Studio but only got one subfolder in the resulting GitHub repository. git status showed that the published subfolder was a submodule with pending changes. Strangely, there was no .gitmodules file for submodule registration. There was, however, another .git directory inside that folder - it was actually a nested repository. To fix that accident, we:

1. Deleted the subfolder's .git directory
2. Removed the submodule from the outer repository's Git index with git rm --cached theFolder
3. Committed the change
4. Added the subfolder back, now as a plain directory, with git add theFolder
5. Committed the change