It would be great if you implement a configuration to switch off the submodule support for the whole SourceTree or for particular repositories. The customer i am working for at the moment is developing an application using a submodule that is in development as well. So if i pull SourceTree now allways updates the submodule and i have to switch to it and checkout the working branch again. The reason why i switched from tower to SourceTree was "no submodule support".