update-piuparts-setup: start with make clean

avoid installing files that were built for a different PREFIX

Signed-off-by: Andreas Beckmann <anbe@debian.org>
whitespace cleanup

Signed-off-by: Andreas Beckmann <anbe@debian.org>
p-m: split mkdir

handle master-directory and section-directory separately

Signed-off-by: Andreas Beckmann <anbe@debian.org>