Git allows you to include other repositories for your project as a submodule, however, I've encountered an errors. To remove them cleanly, follow these steps below.
- Open root directory of project
cd path/to/project
- Move module to a temporary directory
mv path/to/[module] path/to/[module]_tmp
- De-initialize submodule
git submodule deinit -f -- path/to/[module]
- Remove from Git modules
rm -rf .git/modules/path/to/[module]
- Remove from Git repository
git rm -rf path/to/[module]
- Remove temporary directory
rm -rf path/to/[module]_tmp
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