I have a module already installed in the tree and want to replace it by installation via composer.
The magento hackathon composer installed is used.
Also all symlinks created by the installer are excluded via .gitignore
git rmto remove all existing parts of the module and then
git rm/ unstaging
When the co-developers do an update, in the first step git will delete the old module and then install the new module (after composer update). From this part on, the symlinks are ignored.