packagine: setup: Keep md5 sums of entire conf files

engine-setup keeps the md5 hash of configured files so that
on cleanup we can know if it's safe to delete them or some
manual change was made and we should keep them.

This change makes the code keep the md5 hash of the entire file,
instead of 1000 bytes before.

Change-Id: Ie8dfc2f23d1a395dfb35d12fce97896df057816f
Signed-off-by: Yedidyah Bar David <didi@redhat.com>