clone: use more conventional config/option layering

clone: use more conventional config/option layering

Parsing command-line options before reading from config required careful
handling to ensure CLI options were treated with higher priority.  Read
config first to let parsed CLI naively overwrite matching config values.

Helped-by: Junio C Hamano <gitster@pobox.com>
Helped-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Sean Barag <sean@barag.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>