When downloading mission items from the autopilot we need to retry more
agressively, so use a shorter timeout. If we don't do this, we might not
re-request a mission item in time and the autopilot has already given up
the overall mission transfer.

This fixes the case where a mission request from QGC to autopilot or a
mission item from autopilot to QGC gets lost on the link and needs to be
requested again.

By adding a member variable for the total mission item count, we can
actually correctly estimate the progress.

Fixed bugs the unit test found

Also fixed bug with ArduPilot guided waypoint write which would trash
existing mission.

Remove/comment off debug output pollution

This time to handle correctly updating plan/fly view when plan changes

Works around ArduPilot strangeness with empty missions end

Must memset structures before use.

Fixed a pile of bugs as well

Plus low battery announce changes