If we change mode while waiting for waypoints then we are no longer running the mission and should fail

common.py:wait_altitude contained an if statement that, if the plane was changing altitude at all would reset tstart, making the timeout effectively useless. Removing this line allows wait_altitude to respect the timeout the user sets.

this removes the debug code now that the issue has been found (it was
an old version of pymavlink causing the problem)

added tests for FBWB, STABILIZE, CRUISE, ACRO and CIRCLE

check each of the sub-tests pass for overall pass

this enables the register level SITL code

Had to disable check of current WP. Going into auto mode executes commands right away and the reported index will differ per mission. Multiple commands may be executed.

this allows fly.ArduCopter to pass again