The AU tools under development may update and add to the files installed by the native installer. When an uninstall is carried out, it currently only deletes the files that were originally placed there by the installer (in the case of MSI anyway). Ideally it would delete the entire 'app' directory. This should be the same on all platforms.

It is possible that an app will write files to it's working directory so the uninstall should delete these as well.