At the end of October I installed POPFile. Today I just upgraded it to v0.20.1. Just like the install of POPFile, to upgrade it is not an 'easy' thing to do. Here is how you upgrade POPFile on OS X:

Shutdown POPFile, go to http://localhost:8080/ (or the port number you changed POPFile to) and click "Shutdown POPFile"

Backup your current POPFile install. This is at /Library/POPFile

Keep the folder /Library/POPFile/corpus handy, you will need to move this to the new version of POPFile. Also keep "popfile.cfg" which holds your settings.

Download the new version of POPFile

Replace the contents of the /Library/POPFile folder with the contents of the newly downloaded version of POPFile (I trashed the contents and replaced it with the new version of POPFile).

Be sure to move the corpus folder over to /Library/POPFile and the popfile.cfg file, or you will have no buckets, magnets, or anything for that matter!

Open the Terminal and type/paste these two commands:

cd /Library/StartupItems/popfile

sudo sudo ./popfile start

(You will have to authenticate sudo with your password)

Now go to http://localhost:8080/ and you should see the default style'd POPFile History page. I do not know how to copy over the preferences for the style, or for that matter, the configuration page. I tried copying over the "popfile.cfg" file from the old install with no luck. I am going to email the developer about this, and will post it here when I find out.

UPDATE
My problem was the fact that I did not restart the server after I copied over the popfile.cfg file. All is well now, I double checked it.

I had to go to the Configuration page and turn OFF Subject line modification, because I do not use this, and it is ON by default. Figuring out how to copy over the configuration from the old install will fix this problem.

I opened up Mail, and all was well, it works, and is still classifying SPAM as good as before. This entire process did not take very long at all. It has taken me exponentially longer to write about it.

POPFile does a much better job at classifying mail then Mail's Junk Mail Filter. I very rarely have to reclassify mail, and when I do I am saying it is SPAM, I am not getting false positives. I have gotten a few, that is going to happen, but it is few and very far between. I would say more then half the mail I have to "reclassify" has not been classified at all by POPFile (it does not put it into any bucket).