PCI: altera: Move retrain from fixup to altera_pcie_host_init()

Previously we used a PCI early fixup to initiate a link retrain on Altera
devices.  But Altera PCIe IP can be configured as either a Root Port or an
Endpoint, and they might have same vendor ID, so the fixup would be run for
both.

We only want to initiate a link retrain for Altera Root Port devices, not
for Endpoints, so move the link retrain functionality from the fixup to
altera_pcie_host_init().

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