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

Poll for link training status is cleared before poll for link up status.
This can help to get the reliable link up status, especially when PCIe is
in Gen 3 speed.

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