The code where Arduino communicates with Pixhawk does not compile

Post the full error message.

Move PixhawkArduinoMAVLink.cpp and PixhawkArduinoMAVLink.h to src and remove /src from the includes in PixhawkArduinoMAVLink.h

It compiles for me. I do get a lot of warnings, though. I don't have the hardware to test.