clean.c, ls-files.c: respect encapsulation of exclude_list_groups

Consumers of the dir.c traversal API should avoid assuming knowledge
of the internal implementation of exclude_list_groups.  Therefore
when adding items to an exclude list, it should be accessed via the
pointer returned from add_exclude_list(), rather than by referencing
a location within dir.exclude_list_groups[EXC_CMDL].

Signed-off-by: Adam Spiers <git@adamspiers.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>