Clipping a wing won't stop them from a flapping jump, they just have to work harder. Fasten a net or a prefab chainlink panel to the top of your run and then it's not a issue plus it's more secure. If there is a critter in the pen, they will clear your fence. Also if the birds are happy and have plenty of room, they are less likely to try to escape. Maybe a roost hung thru the wire in the run, with a top, will pacify their desire to perch rather than sit in the sunshine plus it gives them some safety if something gets into the run.
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