mc_pos_control: Improve use of local position reference height

1) Don't use when invalid
2) Don't use when in manual mode to prevent jumps if the EKF starts using GPS in flight.

src/modules/mc_pos_control/mc_pos_control_main.cpp

@@ -795,17 +795,26 @@ MulticopterPositionControl::update_ref()
 		if (_ref_timestamp != 0) {
 			/* calculate current position setpoint in global frame */
 			map_projection_reproject(&_ref_pos, _pos_sp(0), _pos_sp(1), &lat_sp, &lon_sp);
-			alt_sp = _ref_alt - _pos_sp(2);
 		}
 
 		/* update local projection reference */
 		map_projection_init(&_ref_pos, _local_pos.ref_lat, _local_pos.ref_lon);
-		_ref_alt = _local_pos.ref_alt;
+
+		/*
+		 * If we are in an auto control mode, correct the altitude reference using the local position
+		 * reference if it is global. In manual control modes we are not interested in absolute altitude
+		 * and need to avoid the jump in estimator height reference that occurs when it starts using GPS
+		 * mid-flight and sets the EKF local frame origin.
+		 */
+		if (_mode_auto && _local_pos.z_global && (_ref_timestamp != 0)) {
+			alt_sp = _ref_alt - _pos_sp(2);
+			_ref_alt = _local_pos.ref_alt;
+			_pos_sp(2) = -(alt_sp - _ref_alt);
+		}
 
 		if (_ref_timestamp != 0) {
 			/* reproject position setpoint to new reference */
 			map_projection_project(&_ref_pos, lat_sp, lon_sp, &_pos_sp.data[0], &_pos_sp.data[1]);
-			_pos_sp(2) = -(alt_sp - _ref_alt);
 		}
 
 		_ref_timestamp = _local_pos.ref_timestamp;