And the only thing (as far as I know) that you would want to keep between versions and not get deleted has been thought of and solved, user-imported libraries. So there really isn't any drawback to having everything contained in an application.
And the only thing (as far as I know) that you would want to keep between versions and not get deleted has been thought of and solved, user-imported libraries. So there really isn't any drawback to having everything contained in an application.