It used to be that if "--all", "--depth", and also explicit references
were sought, then the explicit references were not handled correctly
in filter_refs() because the "--all --depth" code took precedence over
the explicit reference handling, and the explicit references were
never noted as having been found.  So check for explicitly sought
references before proceeding to the "--all --depth" logic.

This fixes two test cases in t5500.
Signed-off-by: NMichael Haggerty <mhagger@alum.mit.edu>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>