1. A method of predicting a trajectory of an aircraft and operating the aircraft, comprising: receiving, at a processor, information defining how the aircraft is to be flown during an operation interval, and storing the information in an information database; deriving, by the processor, a set of instructions from the information stored, wherein the set of instructions comprise configuration instructions that describe an aerodynamic configuration of the aircraft and motion instructions that control an aircraft motion, wherein the aerodynamic configuration comprises a physical configuration of at least one of a high lift device of the aircraft, a landing gear of the aircraft, and a speed brake of the aircraft; confirming, by the processor, that the set of instructions comply with a set of rules stored in a rules database, that the configuration instructions define the aerodynamic configuration of the aircraft and that the motion instructions close degrees of freedom of equations of motion used to describe the aircraft motion during the operation interval; thereafter formulating, by the processor using the set of instructions, an aircraft intent; solving, by the processor, a trajectory optimization problem defined by the aircraft intent according to a predefined criterion to obtain an optimized trajectory; and operating the aircraft according to the optimized trajectory.