MAVLink: Making the mavgen_java.py output match the current state of the Mavlink Library
MAVLink: Add support for the current state of ArduPilot MAVLink files.

The common.xml file was downloaded from https://github.com/diydrones/ardupilot/commit/320834a5e75ca19b5e878258baceaeee3624dca3.

All other messages where generated via generateMessages.py
MAVLink: Quick fix to make the MAVLink library compile.

Further debbuging is needed to make MAVLINK_MSG_ID_DATA_TRANSMISSION_HANDSHAKE work
Core: Switch the RegionOfInterrest object to be a MAV_CMD_DO_SET_ROI command