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.

I mean, that's exactly how kcal count is measured - a portion of food is burnt and the energy released is then measured.

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.

https://en.wikipedia.org/wiki/Calorimeter

Isn't that how all food is measured though?

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.

It is burned to measure total energy and then a model is applied to approximate the calories available to the body.

That's how it was measured, once. Now it is measured based on the components of the food (fat, carbohydrates, and protein).