Copter: CMD dataflash logs use uint16 for total and num
Plane: CMD dataflash logs use uint16 for total and num

Also bug fix for Log_Write_Cmd definition when logging disabled
Plane: remove unused nonnav_command variables

non_nav_command_ID and next_nonnav_command variables removed
Plane: bug fix for setting flight_stage based on current command
Copter: init cmd before saving with Ch7/Ch8
Plane: remove some comments in commands_logic.pde
Plane: remove unused WAIT_COMMAND
Mission: num_commands returns uint16
Rover: create Mission object
Rover: Mission integration with GCS_Mavlink.pde
Rover: Mission integration into command execution
Rover: Mission integration into dataflash Logging
Rover: Mission integration for ch7 save waypoint
Rover: Mission integration for cli test
Rover: remove unused definitions