Clone new repository
$ git clone --no-hardlinks original-repo copied-repo
Filter out the files you want to keep and remove the others
$ cd copied-repo
$ git filter-branch --subdirectory-filter sub/module/path HEAD -- --all
$ git reset --hard
$ git gc --aggressive
$ git prune
$ git remote rm origin
Push the new repositories to the upstream server
$ git remote add origin git@github.com:korya/submodule-repo.git
Add the new repository as submodules to the original repository
$ cd original-repo
$ git rm -r sub/module/path
$ git commit -m "Removing the folders that are now repositories"
$ git submodule add git@github.com:korya/submodule-repo.git sub/module/path
$ git submodule init
$ git submodule update
$ git add .gitmodules sub/module/path
$ git commit -m "Added in submodules for removed folders"
