merge_content(): Check whether D/F conflicts are still present

merge_content(): Check whether D/F conflicts are still present

If all the paths below some directory involved in a D/F conflict were not
removed during the rest of the merge, then the contents of the file whose
path conflicted needs to be recorded in file with an alternative filename.

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