dir: include DIR_KEEP_UNTRACKED_CONTENTS handling in treat_directory()

dir: include DIR_KEEP_UNTRACKED_CONTENTS handling in treat_directory()

Handling DIR_KEEP_UNTRACKED_CONTENTS within treat_directory() instead of
as a post-processing step in read_directory():
  * allows us to directly access and remove the relevant entries instead
    of needing to calculate which ones need to be removed
  * keeps the logic for directory handling in one location (and puts it
    closer the the logic for stripping out extra ignored entries, which
    seems logical).

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