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Fixes a regression from 8bae4e5c0e29f70d5d1d2427ffdef97092be939c, where the orbit flight task wasn't an extra task (flight_tasks_to_add) anymore and therefore the command handling wasn't generated. There was a race condition that could cause several outcomes. The most severe was that flight_mode_manager gets the command, switches to orbit and then in the next iteration switches back because commander did not change nav_state yet. When commander then switches, flight_mode_manager would still be in the old mode. This is prevented by storing the command (allowing it to arrive before or after mode switch), and then apply it after the switch happens.