I am planning to make a boat wich will be on the water for a long time. That includes reboots (in rough waters)! What is the most elegant way to reboot the system regarding IMU / Compas (?) calibration and usage of EK2 / EKF?
is there a way start the system armed and in a specific mode? (would not be too terrible, since a raspberry pi is already handling the modes.
The transmitters failsafe is called throttle failsafe. That is if the throttle PWM input level falls below a certain point i.e. goes to 0 because the transmitter is turned off then the Rover will go into failsafe. To disable this simply set FS_THROTTLE_ENABLE to 0.
You can send a reboot command over MAVLink. If your using MissionPlanner there should be a reboot button in there which does just this.
There is a parameter INITIAL_MODE which will set which mode the Rover defaults to on startup. If however you have an RC Transmitter connected and are using the MODE_CH with a switch to control modes the Rover will go into whatever mode the Transmitter is set to.
For starting up ARMed if you have a safety switch installed you will need to disable it. Set BRD_SAFETYENABLE to 0. You will also need to disable arming with ARMING_REQUIRE set to 0. Note it will still do the arming checks as the parameter ARMING_CHECK is set to 1 which is good but any failures in the checks will only be reported and not prevent arming.