Is there a reason that Thunderbird doesn't seem to be storing these tags in the header of messages on the IMAP server (AFAIK, the server does support this)?
It seems the TaQuilla (and possibly manual as well) tags are only being stored in the .msf.
It is my understanding, however, that Thunderbird does support storing tags in messages headers server-side for IMAP servers that support this.
This would be very useful for those needing to access email from multiple machines – this would at least allow them to be able to see the applied tags…
…syncing training data between hosts would be a whole different (but still useful) issue (is Mozilla Weave coming to Thunderbird??? =)
I am generally familiar with the IMAP issues here. TaQuilla lets the folder save the keywords, which under IMAP is supposed to then add those keywords to the custom message flags if the IMAP server supports it.
So I have tried to do the right thing, and TaQuilla should act no differently than manual tagging. If you can demonstrate that TaQuilla acts differently than manual tagging though, I would be interested to know that.