On 17 Sep 2016, at 1:57, Robert Brenstein wrote:

I just realized that moving to junk mailbox and marking as junk are 2 different and independent things. Does anybody knows what triggers each? I expected mail moved to the junk mailbox automatically tagged as junk

That's correct.

and mail tagged as junk automatically moved to the junk mailbox.

That's not correct. Using “Message ▸ Junk State ▸ Junk” only marks it as junk (with the “standard” `$Junk` IMAP keyword).

Well, I should add that indeed sometimes moving a message to the junk mailbox marks it as junk as well.

That should work every time. It might help to enable the “Raw Flags” column in the messages list if you want to see exactly which flags have been applied.

There is also usability issue. I can put messages into the junk mailbox using the button on the toolbar, the right-click popup on the message, or an item in the message menu. However, it seems that the only way to mark message as junk is to actually open it and click "mark as junk" on the yellow bar, which seems to be shown only for messages that are already in the junk mailbox (when I click move to junk while having the message open, the yellow bar does not appear until I close the message and open it again).

Confusing and mysterious...

Ah, it's a single message window issue. In the main window the email would be moved out of the currently displayed mailbox and therefore it does not have this issue. I've noted this.

The reason for my struggle is that I am trying to set up smart mailboxes that exclude junk mail. I can easily set up a condition to exclude mail flagged as $Junkk but I do not see a way to say: show all mail in this mailbox excluding mailbox Junk.

By default, the Junk mailbox is excluded from most mailboxes including “All Messages”, but the Mailboxes pane in the mailbox editor also allows you to use a “None” group method which allows you to do something like this:

                Some Mailbox

This can be a bit tricky to decipher, but think of it like this: A message must be in both “Some Mailbox” *and* in none of the other mailboxes (which only includes “Junk”).

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