What might have wings for doing bird flap (4)
I believe the answer is:
stir
I believe this is a double definition.
'what might have wings for doing bird' is the first definition.
(a prison - 'bird' can mean a prison sentence)
'flap' is the second definition.
(both can mean to flutter)
(Other definitions for stir that I've seen before include "jug" , "beat" , "Shake up" , "What keeps those inside" , "Thrill" .)