Gitmodules - Git Sub Modules - are really the bane of my life! The recent Drupal 9 update has brought this into sharp focus and pushed us to find a better way of dealing with these. Here is a recipe...
Delete the .git folder of the submodule with the following
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rm -rf public_html/modules/contrib/module_name/.git
rm cached it out of there with this:
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git rm --cached public_html/modules/contrib/module_name
-remove the directory from the main git repo
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rm -rf .git/modules/public_html/modules/contrib/module_name
re-add module explicitly
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Submodule of module_name module should now be untracked so we can add it as files and directory as part of this local repository.
git add public_html/modules/contrib/module_name
Commit the changes
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A piece of cake - just follow these detailed steps for each pesky gitmodule you have and you will be free - probably.