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I don't know why the extended Yoda & Dooku fight, "the lost twenty" and the Jedi raid on the droid ship wasn't in the AOTC DVD. That's something that has to be put in the blu-ray Saga Boxset in 2007.
I believe the box set will be regular DVD, not Blu-Ray. As far as I know, Blu-Ray and HD-DVD are trying to come together right now.