Security Upgrade Overwrites MySQL Config

[Donald Perkovich <donp@mindspring.com>]

I have MySQL 4.1 running in Sarge.  The other day I did a security
upgrade on MySQL and it overwrote the server's my.cnf.  The only
change it made was to the basedir, but that was a huge change since the
server was trying to use a non-existent database.  After a little
checking I discovered the problem and fixed it.

Is there a way to prevent an upgrade from overwriting my config files?
Or do I just have to be aware of the problem and check for it?

Don