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To troubleshoot, first decide if you actually want to use a submodule, which is a Git project inside a Git project; submodules are sometimes created accidentally.
If you don't want to use a submodule, remove the submodule, replacing PATH-TO-SUBMODULE with the path to the submodule:
$ git submodule deinit <em>PATH-TO-SUBMODULE</em>
$ git rm <em>PATH-TO-SUBMODULE</em>
$ git commit -m "Remove submodule"
$ rm -rf .git/modules/<em>PATH-TO-SUBMODULE</em>