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You need to remove the folder from your local repository with git rm -r folderName and then git commit -m 'Delete folder folderName because foo (for example) and git push.
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# the -r option will recursively delete the folder
git rm -r folder-name
# commit changes
git commit -m "Remove duplicated directory"
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sql
git rm -r one-of-the-directories // This deletes from filesystem
git commit . -m "Remove duplicated directory"
git push origin <your-git-branch> (typically 'master', but not always)