I would like to share a workaround. You can clone the entire repo, and then create a symulink for subdirectory:
mkdir <repo_dir>
cd <repo_dir>
git clone <repo_url>
ln -s <sub_dir> <your_location_where_you_want_to_checkout_sub_dir>
Again, this is not a solution - just a workaround. You will still clone the whole repo, and you can pull the changes only from . However, this was useful in some case of mine.