WARNING: If you're running Message Sniffer via the command line and added Message Sniffer to your SpamAssassin-Based Pattern Matching local.cf file you will have to add the rules back to the local.cf file any time you update or re-install SmarterMail.
I set up a test, and SmarterMail overwrites the local.cf file. I tried to make the local.cf file read-only and the upgrade threw an error.
So just remember to add the Message Sniffer rules back into the local.cf after any re-install or upgrade.
SmarterTools: I think this is a bug. The local.cf file should be a persistent file in any SpamAssassin installation and an sa-update, etc. should not touch that file. I think your installer should check to see if a local.cf exists and if so do not overwrite it.