We use submodules to keep track of Core plugins which are in their own repositories. We also use submodule for the UI screenshot tests.

I update all submodules with:

git submodule foreach git pull origin master

A new feature of GIT could be useful to us: http://stackoverflow.com/questions/9189575/git-submodule-tracking-latest/9189815#9189815

When making changes in a submodule

cd plugins/TreemapVisualization
git checkout master
# make change
git push origin

Then tell piwik to track the updated version:

$ cd ../../
$ git add plugins/TreemapVisualization
$ git commit -m "useful msg here"
$ git push

We should document this in a dev page such as http://piwik.org/participate/development-process/