How to remove git submodules? Command init and deinit is very important. Here are some userfull snippets:

git submodule deinit --all -f
git rm sm/my-submodule

Commit chages:

git commit -m "Remove submodule sm/my-submodule"

Clear git cache for this submodule:

rm -rf .git/modules/sm/my-submodule
git status

If you want to replace removed submodule with corresponding files, then add files. Copy submodule files by hand into specific directory. 

cp ../tmp/my-submodule-file.txt sm/my-submodule-file.txt
git add .

Finalize Repo:

git submodule deinit --all -f
git submodule init
git submodule update --recursive --remotea

Repo should be pushed and carefully pulled if necessary.