I've been able to successfully get waypoints off of the Pixhawk using a series of mission_request_list, then waiting for the count and then sending a mission_request how every many times the count it I received.
However, I'm still having trouble with sending a list of waypoints to the Pixhawk. If I send a mission_count message, the Pixhawk responds with mission_request messages, but it doesn't seem to get the mission_item messages I send to it after that. It just keeps sending mission_request items with sequence 0 as it never gets the first one.
Does anyone have any ideas I can try with this?