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Dave Allen, I think, published an article that noted a drastic change in the movement of Lee's cut fastball. That was the key.
It's not really going to show up in the Pitch Type data, except in terms of better run values. Neither will command.
Fangraphs' data is superb, but certainly not comprehensive.
....
As to '08, undoubtedly the new, devastating cutter was getting identified as a fastball.