PCIe: fix double initialization bug

Earlier patches to split out the hardware init for PCIe hotplug resulted in
some one-time initializations being redone on every resume cycle.  Eg.
irq/polling initialization.

This patch splits the hardware init into two parts, and separates the
one-time initializations from those so that they only ever get done once,
as intended.

Signed-off-by: Mark Lord <mlord@pobox.com>
Signed-off-by: Andrew Morton <akpm@linux-foundation.org>
Signed-off-by: Kristen Carlson Accardi <kristen.c.accardi@intel.com>
Signed-off-by: Greg Kroah-Hartman <gregkh@suse.de>