Dead city once covered by rock and dirt (6)
I believe the answer is:
ordure
'dirt' is the definition.
(I've seen this before)
'dead city once covered by rock' is the wordplay.
'dead' becomes 'd' (abbreviation in government records).
'city once' becomes 'ur' (ancient Sumerian city state).
'covered by' is an insertion indicator.
'rock' becomes 'ore' (ores are found in rocks).
'd'+'ur'='dur'
'dur' put into 'ore' is 'ORDURE'.
'and' acts as a link.
(Other definitions for ordure that I've seen before include "Dung, filth" , "unclean" , "Dirt" , "Excrement" , "soil" .)