No, I never get the APM flow chart.  Why should I ask them if I had them already?

May be I don't understand your question.

I am looking for one also.

Hey Patrick, I was wondering if you were available to answer a couple questions for me.  I am trying to do something very similar to you with ROS and I am wondering what all you have achieved so that I don't have to reinvent the wheel, so to speak.  I am going to have a ROS node sending waypoints (as MAVlink messages) to our APM via XBEE serial comm.  Also, my ROS node will be listening for GPS coords (as MAVlink messages) that will be sent from the APM to ROS.  Have you been able to get row-mavlink-pkg running? Have you figured out the best way to send MAV messages from the APM?