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When a new instant message arrives while using Empathy with Gnome Shell, it is marked as an unread message by Empathy, triggering a changed icon for the Contact List. In addition, a Gnome Shell notification is triggered, attached to an icon for the sender. Reading the message in one of these two locations does not clear the notification in the other location, resulting in out-of-date unread counts and redundant information being presented to the user.
Wow, this is one HIGHLY annoying bug for a user. Getting the message prompts twice, even when the *client settings* are saying to disable all forms of notifications. If they want to integrate Empathy and GNOME Shell, settings should use one window or the other. The notifications should also honour the *client settings* for notification messages. Also, see this upstream GNOME bug report also https://bugzilla.gnome.org/show_bug.cgi?id=632726
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