repo=<Repo Name>
name=<Folder Name>

git remote add $name $repo
git fetch $name
git branch tmpbranch $name/master
git checkout tmpbranch
mkdir $name/
git ls-tree -z --name-only HEAD | xargs -0 -I {} git mv {} $name/
git commit -m "Moved files to sub dir/"
git checkout master
git merge -m 'merge repo' --allow-unrelated-histories tmpbranch
git push
git remote remove $name
git branch -d tmpbranch