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I have approached the idea from a different, and I think better, angle. All mail which SpamAssassin things is spam has an X-Spam-Flag: YES header, and mail which it thinks is ham has a X-Spam-Flag: NO header. So, if I just tell users to move any misfiled mail into the right folder, I can then look through it for headers which don't match the folder.
To that end, I have written a bash script to do that very job, and placed it on GitHub at cyrus-mark-ham-spam. -