isci: fix 'link-up' events occur after 'start-complete'

isci: fix 'link-up' events occur after 'start-complete'

The call to wait_for_start() is meant to ensure that all links have been
given a chance to come up before letting the kernel proceed with
probing.  However, the implementation is not correctly syncing with the
port configuration agent.  In the MPC case the ports are hard-coded, in
the APC case we need to wait for the port-configuration to form ports
from the started phys.

Towards that end increase the timeout for the APC agent to form ports,
and delay start complete until all phys are out of link-training.

Cc: <stable@vger.kernel.org>
Cc: Richard Boyd <richard.g.boyd@intel.com>
Signed-off-by: Dan Williams <dan.j.williams@intel.com>