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I just posted something from the 9/11 Commission Report that will be of interest to this thread...

Page 117

Mary McCarthy, the NSC senior director responsible for intelligence programs, initially cautioned Berger that the “bottom line” was that “we will need much better intelligence on this facility before we seriously consider any options.” She added that the link between Bin Ladin and al Shifa was “rather uncertain at this point.” Berger has told us that he thought about what might happen if the decision went against hitting al Shifa, and nerve gas was used in a New York subway two weeks later.44

Page 128

The original sealed indictment had added that al Qaeda had “reached an understanding with the government of Iraq that al Qaeda would not work against that government and that on particular projects, specifically including weapons development, al Qaeda would work cooperatively with the Government of Iraq.”109This passage led Clarke, who for years had read intelligence reports on Iraqi-Sudanese cooperation on chemical weapons, to speculate to Berger that a large Iraqi presence at chemical facilities in Khartoum was “probably a direct result of the Iraq–Al Qida agreement.” Clarke added that VX precursor traces found near al Shifa were the “exact formula used by Iraq.”110This language about al Qaeda’s “understanding” with Iraq had been dropped, however, when a superseding indictment was filed in November 1998.111

The original sealed indictment had added that al Qaeda had “reached an understanding with the government of Iraq that al Qaeda would not work against that government and that on particular projects, specifically including weapons development, al Qaeda would work cooperatively with the Government of Iraq.”109This passage led Clarke, who for years had read intelligence reports on Iraqi-Sudanese cooperation on chemical weapons, to speculate to Berger that a large Iraqi presence at chemical facilities in Khartoum was “probably a direct result of the Iraq–Al Qida agreement.” Clarke added that VX precursor traces found near al Shifa were the “exact formula used by Iraq.”110This language about al Qaeda’s “understanding” with Iraq had been dropped, however, when a superseding indictment was filed in November 1998.111

So Clarke and Berger both knew about the Saddam-al Qaida connection - not some tenuous connection but "the agreement" (“probably a direct result of the Iraq–Al Qida agreement.” ) and Iraqi WMD (VX precursor traces found near al Shifa were the “exact formula used by Iraq.”).

Guess I missed that.