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It is likely that Bush will pardon everyone who worked for him, which is one of his powers as President. That does not preclude doing what Desmond Tutu did after the end of apartheid. The people who committed crimes in the former government were given the chance to testify as to what they had done. There may not need to be a commission independent of Congress. The new Congress can call the people who committed the crimes (Addington, Yoo, Goodling, Gonzales, even Cheney) and compel them to testify. Given that they have immunity to their crimes but not to perjury and contempt, they would have to testify or go to prison -- not for old crimes but for new ones. They can be held in contempt, I think, for a year of imprisonment. Perjury has a much longer sentence.
We need to know what these buzzards did when they were messing with the Constitution. We need to know what they did to the Justice Department, which the new President is going to have to totally clean up from top to bottom. And Justice needs to act as enforcer for the Congressional investigation. If we don't know, there is not going to be the safeguard against another fascist dictatorship should it arise.