To remove a submodule you need to:

  1. Delete the relevant section from the .gitmodules file.
  2. Stage the .gitmodules changes git add .gitmodules
  3. Delete the relevant section from .git/config.
  4. Run git rm –cached path_to_submodule (no trailing slash).
  5. Run rm -rf .git/modules/path_to_submodule
  6. Commit git commit -m “Removed submodule "
  7. Delete the now untracked submodule files
  8. rm -rf path_to_submodule

See also: alternative steps below.