Regression makefile now needs to make separate lists of what to clean

Regression makefile now needs to make separate lists of what to clean
for input/ and output/ directories, because with the addition of
largeobject_1.source, they're not the same list.  Apparently the current
buildfarm process does not exercise whether 'make distclean' leaves a
clean tree behind, else the farm would have been failing for awhile.