PCI: altera: Poll for link up status after retraining the link

Some PCIe devices take a long time to reach link up state after retrain.
Poll for link up status after retraining the link.  This is to make sure
the link is up before we access configuration space.

[bhelgaas: changelog]
Signed-off-by: Ley Foon Tan <lftan@altera.com>
Signed-off-by: Bjorn Helgaas <bhelgaas@google.com>