clean: consolidate handling of ignored parameters

clean: consolidate handling of ignored parameters

I spent a long time trying to figure out how and whether the code worked
with different values of ignore, ignore_only, and remove_directories.
After lots of time setting up lots of testcases, sifting through lots of
print statements, and walking through the debugger, I finally realized
that one piece of code related to how it was all setup was found in
clean.c rather than dir.c.  Make a change that would have made it easier
for me to do the extra testing by putting this handling in one spot.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>