Softly cried out like a bird shut in (6)

'shut in' is the definition.
(thesaurus)

'softly cried out' is the wordplay.
'softly' becomes 'p' (short for piano, musical term for softly).
'cried' becomes 'cooed' (I can't justify this - if you can you should give a lot more credence to this answer).
'out' indicates putting letters inside.
'p' placed inside 'cooed' is 'COOPED'.

'like a bird' is the link.
I am not very happy about this link. Some or all of it may be part of another bit of the clue.

Can you help me to learn more?