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Just documenting this in case anyone else tries it :)
I spent a couple of hours seeking to get a Fieldfield to work with Ctools' dependency functionality. Even with Eclipse, I ran into problems with conflicts in the #process side of things. In the end, I found a simple workaround: In form_alter, shift the filefield into a fieldset and apply the dependency to the fieldset. If you don't put a title on the fieldset, and style it to have no margin/border/padding, you'll get the same effect with far fewer headaches.