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DoD has been organized, trained and equipped to fight big armies, navies and air forces. It is not possible to change DoD fast enough to successfully fight the global war on terror; an alternative might be to try to fashion a new institution, either within DoD or elsewhere — one that seamlessly focuses the capabilities of several departments and agencies on this key problem.
In other words, nothing is Rumsfeld's fault and in fact he probably needs his own personal para-military strike force under his personal command to avoid all those pesky DoD people whose advice he keeps ignoring.