IB/hfi1: tune_pcie_caps is arbitrarily placed, poorly

The tune_pcie_caps needs to occur sometime after PCI is enabled, but
before the HFI is enabled.  Currently it is placed in the MSIx
allocation code which doesn't really fit. Moving it to just after
the gen3 bump.

Clean up the associated code (modules, etc.).

Reviewed-by: Mike Marciniszyn <mike.marciniszyn@intel.com>
Reviewed-by: Sadanand Warrier <sadanand.warrier@intel.com>
Signed-off-by: Michael J. Ruhl <michael.j.ruhl@intel.com>
Signed-off-by: Dennis Dalessandro <dennis.dalessandro@intel.com>
Signed-off-by: Doug Ledford <dledford@redhat.com>