"When the storm comes, You can never hide... only run"
-me, just now
When the covenant first started their assault upon humanity It was made crystal clear things like bomb shelters had little to no use when they started glassing. No one could truly survive once a planet was glassed and shelters just gave you a grave to put your self in. I suggest we have a Defence Research Branch for Evacuations.
To start it you require two civic labs
The First level makes it so a third of your population will leave the planet when it starts becoming bombarded and will be sent to the closest ally owned planet. if the attack stops or if the planet is once again owned by you the population that was rescued will return allowing for the planet to repopulate and rebuild a little quicker.
A Second upgrade Will allow each ship sent out to have two Longswords body guards that will attack any vessel who targets it.
Note flood can infect the trasport vessels and if one lands on a planet infected you will loose the planet, but the ships are slow moving and will allow ou to send a strike craft to destroy it before causing damage.