The tutorial on the developer wiki is kinda lame (I wrote it so I can say that). I might update that with our latest code to "fix" the crouch jump bug. Basically what the code is supposed to do is provide a linear ramp-up / down to the duck position while you in jumping instead of the pop that is performed by HL2. The idea was that this would fix hit reg issues with the hitboxes popping way above the player during crouch jump maneuvers. Extensive testing performed since our implementation realized that the ramp-up / down only fixes half the problem, the other half you'll have to do with a crouch-jump animation that keeps the player's body in check during the maneuver.
Jonathan White <KillerMonkey> GoldenEye: Source
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