Allan, Dr. Drang,
FWIW, the Subversion bundle works exactly the same way. If you commit from a text file, it only tries to commit said text file; if you want to commit a folder or the whole project, you have to click the appropriate place in the project pane.
So the git bundle behaves just like the Subversion bundle, which is both good because it's consistent and bad because obviously people get confused (I got confused by that, too). Whatever changes you make to the git bundle, should also be made to the Subversion bundle or else you end up with the versioning bundles behaving all differently.
That said, I'd suggest something else - why not make the menu item "commit" automatically commit the whole project and add a new menu item "commit this file only"? I figure most people will want to commit all pending changes at once most of the time, and if you need to only commit the single file, you can still do so.
Any thoughts from the list?
Thorsten