powerpc/eeh: Check PCIe link after reset

After reset (e.g. complete reset) in order to bring the fenced PHB
back, the PCIe link might not be ready yet. The patch intends to
make sure the PCIe link is ready before accessing its subordinate
PCI devices. The patch also fixes that wrong values restored to
PCI_COMMAND register for PCI bridges.

Signed-off-by: Gavin Shan <shangw@linux.vnet.ibm.com>
Signed-off-by: Benjamin Herrenschmidt <benh@kernel.crashing.org>