Prosecuting all detainees in federal courts raises a host of problems. Evidence gathered through military interrogation or from intelligence sources might be thrown out. Defendants would have the right to confront witnesses, meaning undercover CIA officers or terrorist turncoats might have to take the stand, jeopardizing their cover and revealing classified intelligence tactics.
In theory, Obama could try to transplant the Bush administration's military commission system from Guantanamo Bay to a U.S. prison. But Tribe said, and other advisers agreed, that was "a nonstarter." With lax evidence rules and intense secrecy, the military commissions have been criticized by human rights groups, defense attorneys and even some military prosecutors who quit the process in protest.
What this says to me is that they still want a way to prosecute people against whom the only evidence is extremely dubious, or was extracted through torture.
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