doc: list filter-branch subdirectory-filter first

doc: list filter-branch subdirectory-filter first

The docs claim that filters are applied in the listed order, so
subdirectory-filter should come first.

For consistency, apply the same order to the SYNOPSIS and the script's usage, as
well as the switch while parsing arguments.

Add missing --prune-empty to the script's usage.

Signed-off-by: David Glasser <glasser@davidglasser.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>