ixgbe: Fix copper PHY initialization code

While cleaning up the internal API focussing on Fiber and CX4 code
we found that I had broken the copper PHY initialization code. This
patch restores the PHY-specific code. This is mostly uninteresting
since no copper PHY boards are yet available. The changes have been
tested against Fiber only as I do not even have copper PHY versions
of 82598 macs.

This change actually cleans up the API code a bit more and we
lose some initialization code. A few PHY link detection helper
lines of code have been snuck into this patch, as well as a
read flush where it was suspected that this might cause issues.

Signed-off-by: Auke Kok <auke-jan.h.kok@intel.com>
Signed-off-by: Jeff Garzik <jeff@garzik.org>