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If you want to fully remove a submodule, the following things have to done :

• remove the submodule entry from the .gitmodules file in the root of the main git repo
• remove the variables associated to the submodule
• remove the description in ./git/modules folder
• remove the folder containing the submodule

Assume that the submodule is called submod and that it's path relative to the root of the git repo is external/gits

Open a terminal in the root of the git repo, and edit the .gitmodules file to remove the entry

[submodule "external/gits/submod"]
path = external/gits/submod
url = https://github.com/user/submod.git

Remove git tracking of the submodule folder, but keep the files :

git rm --cached -r external/gits/submod

Remove the submodule from git config (all variables are remove using section) :

git config --remove-section submodule.external/gits/submod

stage and commit the changes in .gitmodules

git add .gitmodules
git commit -m "Remove submodule submod"

Remove the submodules from .git/modules

rm -rf .git/modules/external/gits/submod

Finally, push the changes to the remote repo

git push

Note that the files are still on the host, to remove them just use rm :

rm -rf external/gits/submod