Has foe manipulated good spy holed up here? (4,5)
I believe the answer is:
safe house
'spy holed up here?' is the definition.
(where a spy may be kept safe)
'has foe manipulated good' is the wordplay.
'manipulated' is an anagram indicator.
'good' becomes 'use' (in phrases like 'it's no good', 'any good?' etc).
'has'+'foe'='hasfoe'
'hasfoe' with letters rearranged gives 'safeho'.
'safeho'+'use'='SAFE HOUSE'
(Other definitions for safe house that I've seen before include "Secure hiding place" , "Place used secretly as a refuge" .)