Hi Bogdan,
The tricky thing with the read flags is that they are on a per user basis - so the only possibility is to insert read flags for all users.
And if you add a user later on, he'll still see all system articles as unread, for existing tickets.
I understand the issue with the auto-replies marked as unread by default.
I think I even do not like per se the fact that auto-replies are stored as articles; I think it would be good to have the possibility to directly send the autoreplies, marking them of course in ticket history, but not storing them as articles, what do you think?
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