Understand program, run with what purpose? (9)
I believe the answer is:
apprehend
'understand' is the definition.
(apprehending is a kind of understanding)
'program run with what purpose?' is the wordplay.
'program' becomes 'app' (type of computer program).
'run' becomes 'r' (cricket abbreviation).
'with' means one lot of letters go next to another.
'what' becomes 'eh' (I've seen this in other clues).
'purpose?' becomes 'end' (purpose is a kind of end).
'app'+'r'+'eh'+'end'='APPREHEND'
(Other definitions for apprehend that I've seen before include "Dread; capture" , "bust" , "Catch; understand" , "collar" , "Get the meaning of or take into custody" .)