WHEN PRESIDENT BUSH asked Donald Rumsfeld to come up with a plan to invade Afghanistan and kick al Qaeda out of its hiding places, Rumsfeld and General Hugh Shelton, the chairman of the Joint Chiefs of Staff, said he’d have to wait a while. Though the CIA had been pursuing al Qaeda leads in the region for much of the 1990s and had contingency plans to topple their protectors, the Taliban, the Pentagon had no contingencies for the type of operation the president wanted.