My email from spyderous below and the two bugs here:
https://bugs.gentoo.org/show_bug.cgi?id=80225
https://bugs.gentoo.org/show_bug.cgi?id=98415

On Fri, 2005-07-08 at 19:25 -0600, Tres Melton wrote:
> May I suggest a brief comment for those of us that manually merge all
> config file changes so we (I) know that it was intentional.  It would
> save you a bug report (or two).  :-)     And thanks for the great work.

They're in the ChangeLog. Next time, try looking there! =) Not too tough
to find searching for xsetup and pam, respectively.

  29 Jun 2005; Donnie Berkholz <spyderous@gentoo.org>;
  xorg-x11-6.8.2-r2.ebuild, xorg-x11-6.8.99.13.ebuild:
  Fileset 0.5 for 6.8.2-r2, fileset 0.2 for 6.8.99.13. (#80225) Remove
  Gentoo-specific code from Xsetup_0 and start installing upstream
version
  instead.

  30 May 2005; Donnie Berkholz <spyderous@gentoo.org>;
  xorg-x11-6.8.2-r2.ebuild, xorg-x11-6.8.99.8.ebuild:
  Fileset 0.4 for 6.8.2-r2, fileset 0.2 for 6.8.99.8. (#93920) Don't
specify
  full path to pam modules in /etc/pam.d/ files. It breaks lib64-using
  systems.

Thanks,
Donnie