Refactor: tools: Set call options in cibadmin after option parsing

Do less work during the option parsing stage, get fewer trace messages
when there are conflicting options that override each other, etc.

This also fixes an issue where the cib_multiple flag would be set if
--delete-all appeared anywhere in the argument list. Now, if any other
command option appears after --delete-all, the delete_all flag gets
unset, and cib_multiple does not get set.

Signed-off-by: Reid Wahl <nrwahl@protonmail.com>