As someone else already noted, they use published (kilo)calorie values for the ingredients. Those were determined by burning a quantity of the item in a device called a bomb calorimeter, which measures the total energy released.
The Calorie (the capital letter is important) listed on the label is actually a kilocalorie, or 1000 calories. One calorie is, as was noted by the other commenter, the amount of energy it takes to heat a gram of water by one degree Celsius.
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