Rename manpages in /usr/X11R6/man/man3/ with .man extension to use .3x instead.
Strip shared libraries in /usr/X11R6/lib/.
Strip and chown root.bin /usr/X11R6/bin/ (taking care not to remove setuid
bit from XFree86, xterm, and xload)
Move spare bitmaps in /usr/X11R6/include/bitmaps into
/usr/X11R6/include/X11/bitmaps, make bitmaps -> X11/bitmaps link.
Add symbolic links:
cd usr ; ln -sf X11R6 X11
cd usr/bin ; ln -sf  /usr/X11R6/bin X11 
cd usr/lib ; ln -sf  /usr/X11R6/lib/X11 X11
cd usr/include ; ln -sf  /usr/X11R6/include/X11 X11
Remove links in /usr/X11R6/lib/X11/, move directories in /etc/X11/ to
/usr/X11R6/lib/X11/.
Create /var/X11R6/lib, move contents of /usr/X11R6/lib/X11/ into it,
and put a symlink to /var/X11R6/lib/ at /usr/X11R6/lib/X11/.
Remove /etc/X11 directory, put a link to /var/X11R6/lib/ there.
Move /var/X11R6/lib/xinit/xinitrc to /var/X11R6/lib/xinit/xinitrc.twm,
make xinitrc a link to it.
Add .Xmodmap and README.Xmodmap to /var/X11R6/lib/xinit/.
Edit Xlib.h to #include <stddef.h>
Make font directories in /usr/X11R6/lib/fonts/, add symlink to
this directory in /var/X11R6/lib/.
Remove that bunk /usr/X11R6/lib/libz.a that always gets installed.