Ports/packages confusion

[Chandan Haldar]

Continuing to wallow in my pool of port upgrade sorrows, I'm confused on
a few basic aspects of ports/packages maintenance.  Looked around, but
couldn't find much clarity (may be haven't found the right docs yet).

Will someone please point me to an explanation for why the packages in my
install sets (that I chose at the time of installation of my FreeBSD 6.0 
Release),
for example the X11R6 packages, do not show up in the installed packages
list (pkg_info or pkg_version)?  What will happen to the installed Xorg 
set if
I try to upgrade to a newer Xorg rel through the ports/packages system?

May be this would explain to me how (while trying to upgrade my installed
ports including gnome 2.10->2,12 upgrade) I managed to mess up my working
gnome 2.10 installation (done from the ISO disk images at FreeBSD 
install time)
so badly that I'm finding it impossible to recover from that.  The 
mysteries of
pkgdb -F also needs way more effort than I have been able to give so 
far.  It
shows stale dependnecies right after portsnap fetch/extract even before 
pkg_info
shows any packages installed.  Why?!  Where can I read a precise 
definition of
'stale dependency' as understood by the ports management programs?

At the moment, portupgrade, portmanager, gnome_upgrade.sh (yes, I finally
found that one too), nothing seems to be able to get gnome back up without
throwing me right back into pkgdb -F with a whole bundle of stale 
dependencies
that I do not know how to resolve manually staring at me.  Is 
reinstalling FreeBSD
+ X + gnome + other packages from the Nov 2005 released ISO disk images
my best bet to get back to a working system like I had before I attempted to
upgrade my ports to the latest versions?

I have not been hacking unix for several years recently, but was not 
exactly a
complete newbie once upon a time.  Thanks for any explanation or pointer.

Chandan