It is not a simple Kalman filter. The presented Kalman Navigation filter calculates the position from delta ranges and GPS raw data. The tightly coupling with sensor data allows a precise calculation of the GPS clock error and error drift. With this technique it is possible calculate a navigation solution even if only 3 satelites are visible.
On the other side nonlinear control techniques with neural networks are used (dynamic inversion) to control the airplane.
All this high level algorithms are usually programmed and evaluated in matlab by engeneering scientists. This is the reason for using Matlab/Simulink Coder with RT-Linux hardware to create a one click solution for testing the algorithms in flight.