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"The fact that the DOD, which had made the link between Atta (and other perps?) and AQ, was forbidden to give this info to the DOJ was an unintended consequence."

- I agree 100% with your reasoning.
Any destruction of documents and the closing down of Able Danger before 9/11 was due to the fear in the Clinton Administration that it could turn up linkages between known Chinese operatives and illegal contributions to Slick's campaign. After 9/11, they realized to their horror (with the Able Danger staff briefings to the Commission) that they had at the same time destroyed information that might have prevented 9/11.
My guess is that the Dems and their staff on the Commission made sure that the Able Danger information never reached them directly in testimony so they could retain, "plausible deniability" and the White House/Republicans went along with the cover up because such information could become another Watergate in terms of ripping the country apart - and Bush wanted unity in view of the upcoming war in Iraq.
The secret compromise agreement between the two Party's can be seen in the final Commission Report, which is neutral in assigning blame for 9/11 as between Bush and Clinton.
The unwritten understanding was (I believe):
-Repubs - the report must not assign blame
-Dems - the report is not to mention Able Danger
The question now is: Will both Party's cooperate behind the scenes to shut down loose cannon Weldon, and if so, how?
Stay tuned.