Primarily digestion, but for "left-overs" or food waste and scraps there's vermiculture and composting. I guess we have mass digesters now too to turn the material into heat.
You can't measure nutritional values like that. Not everything that can be burned is available to the human metabolism. Cellulose being one obvious example.
That's true, but we aren't usually burning things that humans would not normally eat. There's a lot of variations on measuring calories (not nutritional value, two different things), but the method of the Calorimeter is pretty standard and in line with the parent's comment.
no, foods are analyzed for their digestible contents (fats, fiber, carbs, various kinds of alcohos etc.) and their energy content is then looked up in reference tables. The reference tables are in turn populated with more careful experiments that take digestion, waste products and metabolic efficiency into account.
Directly measuring the physiological energy content for millions of food products would be impractical.
