Submodules aren’t removed using git rm submodule-dir, they need to be removed in a far more thorough and annoying fashion. There are a number of unclear explanations at various sources so I decided to write my own findings.

  1. Delete the relevant parts from the .gitmodules file.

    EG:

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    [submodule "blog/themes/PaperMod"]
    path = blog/themes/PaperMod
    url = https://github.com/adityatelange/hugo-PaperMod.git

  2. Stage .gitmodules via git add .gitmodules

  3. Remove the relevant parts from .git/config

    EG:

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    [submodule "blog/themes/PaperMod"]
    url = https://github.com/adityatelange/hugo-PaperMod.git

  4. Clear the cache with git rm --cached /path/to/submodule - with no trailing slash. Including the trailing slash will throw an error

  5. Remove the .git modules submodule data by running rm -rf .git/modules/submodule_name or rm -rf .git/modules/submodulefoldername

  6. Commit the changes

  7. Delete the submodule files rm -rf path/to/submodule