As it may happens that the default branch of your submodules are not master
(which happens a lot in my case), this is how I automate the full Git submodules upgrades:
git submodule init
git submodule update
git submodule foreach 'git fetch origin; git checkout $(git rev-parse --abbrev-ref HEAD); git reset --hard origin/$(git rev-parse --abbrev-ref HEAD); git submodule update --recursive; git clean -dfx'