Use a diff for iteration in index_update_all and index_add_all

Without this option, we would not be able to catch exec bit changes.

The functionality was meged without including tests, so let's add them
now.

Attributes: don't match files for folders

Use the packbuilder in local push

The interesting one is the notification macro, which was returning
directly on a soft-abort instead of going through the cleanup.

submodule: add test initialising and cloning a repo

A couple of tests use the wrong remote to push to. We did not notice up
to now because the local push would copy individual objects, and those
already existed, so it became a no-op.

Once we made local push create the packfile, it became noticeable that
there was a new packfile where it didn't belong.

It has now become a no-op, so remove the function and all references to
it.