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I use Thunderbird with gmail via imap and do so with multiple accounts. On the gmail side I have filters that will automatically assign labels to incoming mail and archive it moving it out of the inbox.

On the Thunderbird side it will see the new mail appear in the corresponding folder and the all mail folder -- that's fine but my problem is that they're both marked as unread. Since I have many accounts I use the unread mail view in Thunderbird's folder panel and what I see is both folders highlighted as unread. When I read the message in one folder the other only get marked as read I click on it and Thunderbird does another imap transaction.

Is there a configuration that will recognize the same mail in two different folders automatically?

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I don't think IMAP has the concept of the same message being in two different folders. However, there may be a Thunderbird extension that uses heuristics to handle this, similar to the one used by Remove Duplicate Messages.

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