These operations result in staged but uncommitted changes to your branch; you will need to commit them as normal. Execute them in the root of your checkout.
~/weave$ git submodule add https://example.com/organisation/module vendor/example.com/organisation/module
~/weave$ git submodule foreach git pull origin master
~/weave$ (cd vendor/example.com/organisation/module && git checkout <commit-ish>)
~/weave$ git add vendor/example.com/organisation/module
~/weave$ git submodule deinit vendor/example.com/organisation/module
~/weave$ git rm vendor/example.com/organisation/module
~/weave$ rm -rf .git/modules/vendor/example.con/organisation/module