Spirit runs in by church tower (6)
I believe the answer is:
belfry
'church tower' is the definition.
(I've seen this in another clue)
'spirit runs in by' is the wordplay.
'spirit' becomes 'elf' (I've seen this before).
'runs' becomes 'r' (cricket abbreviation).
'in' means one lot of letters goes inside another.
'elf'+'r'='elfr'
'elfr' going into 'by' is 'BELFRY'.
(Other definitions for belfry that I've seen before include "Place for ringers" , "Church tower space" , "Part of a tower or steeple" , "Bats in the ...... is slangily crazy" , "Interior of a steeple (where bats hang out?)" .)