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Upgrade procedure

Forgive me, but I can't seem to find the emails where the upgrade
procedure was discussed. I have yet to move from RC5 to 4.0.1, and I
want to ensure that I don't lose my configs. I recall in an earlier
version, to upgrade, you had to remember to use make setup instead of
make install, or something similar.

Could someone possibly forward it to me or point me to the proper
archive link? Thanks a ton. 

~Kim