notes-merge: use opendir/readdir instead of using read_directory()

notes-merge: use opendir/readdir instead of using read_directory()

notes_merge_commit() only needs to list all entries (non-recursively)
under a directory, which can be easily accomplished with
opendir/readdir and would be more lightweight than read_directory().

read_directory() is designed to list paths inside a working
directory. Using it outside of its scope may lead to undesired effects.

Apparently, one of the undesired effects of read_directory() is that it
doesn't deal with being given absolute paths. This creates problems for
notes_merge_commit() when git_path() returns an absolute path, which
happens when the current working directory is in a subdirectory of the
.git directory.

Originally-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Updated-by:  Johan Herland <johan@herland.net>
Signed-off-by: Johan Herland <johan@herland.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>