You cook them. Try looking into "decoction mashing", where you boil 40% of your grains, them add them back to the rest of the mash.
Also, most flakes are 'cooked' or gelatinized by the heat of the rolling process. It's what makes Quaker Oats "quick cooking' or 'instant'- they've already been done once.
So far, I've had more experience thinking than I've had brewing....you don't think they are mutually exclusive, do you?
72 batches so far,
48 wine, mostly Loquat, peach, plum, prickly pear
23 beers and ciders
1 Tequila, from a prickly pear wine experiment that didn't work. I call it "Prickly Heat"