Farmer finally runs with it inside sheep pen again (7)
I believe the answer is:
rewrite
'pen again' is the definition.
('write' can be a synonym for 'pen' so perhaps 'rewrite' is OK for 'pen again')
'farmer finally runs with it inside sheep' is the wordplay.
'finally' says to take the final letters.
'runs' becomes 'r' (cricket abbreviation**).
'with' says to put letters next to each other.
'inside' means one lot of letters goes inside another.
'sheep' becomes 'ewe' (I've seen this before).
The last letter of 'farmer' is 'r'.
'r'+'it'='rit'
'rit' inserted into 'ewe' is 'ewrite'.
'r'+'ewrite'='REWRITE'
(Other definitions for rewrite that I've seen before include "Transcribe again" , "Redraft" , "Completely change (script)" , "Revise" , "Produce new draft" .)