After weeks of warning, the time has come. All day Saturday and Sunday, BART will close the Transbay Tube for major track repairs, severing the regional transit system at its backbone and forcing riders onto buses and ferries or into their cars to get between San Francisco and the East Bay. The shutdown underscores the wear-and-tear of an aging system that is more popular than ever, and raises questions about whether agency leaders could have done anything to avoid taking the tube offline for a full weekend.