Home found in a well — pardon? (7)
I believe the answer is:
amnesty
'pardon?' is the definition.
(I know that amnesty is a more specific form of the action pardon)
'home found in a well' is the wordplay.
'home' becomes 'nest' (a bird's home).
'found in' indicates putting letters inside.
'well' becomes 'my' (both are expressions of surprise).
'a'+'my'='amy'
'nest' going within 'amy' is 'AMNESTY'.
(Other definitions for amnesty that I've seen before include "suspension of law" , "Dispensation" , "Men stay (anag.)" , "A general pardon as for rebels (7)" , "International organisation concerned with human rights" .)