The loop contains the body of the Finite state machine code. The actual code for the FSM is in UserFiniteStateMachine.h. Declarations of the I/O and the user variables can be programmed in UserConfiguration.h (or better; added by the Configurator). Mention the call UserFSM() in the loop; this is actually a call to the UserFiniteStateMachine.h software.
Click here for the loop code of the sketch.