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The notification tray at the bottom of my desktop screen gets overcrowded with notification icons after several notify-send messages appear. Is there a way to clear this tray?

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Yes: you can right-click your icons and select "Remove" from the pop-up list:

Menu entry

Alternatively, you can left-click each one and click on its notification bubble to acknowledge and clear it.

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... I think the OP wants a way to clear all notifications all at once... – fossfreedom Nov 29 '11 at 23:08
@fossfreedom Unless there's an extension that does this, I am not aware of any other way to do it out-of-the-box. – Christopher Kyle Horton Nov 29 '11 at 23:16
Is there a way to get Unity to automatically remove notifications from the tray after a certain period of time? – dan Nov 29 '11 at 23:25
@dan AFAIK Unity already gets rid of its notifications after a couple seconds of displaying them. Unless you meant GNOME Shell...then in that case, there's no way to do it from the default install that I know of, unless there's an extension somewhere. – Christopher Kyle Horton Nov 29 '11 at 23:29
It's funny because it didn't do that earlier as far as I can remember. There is also an extension that specifically makes notifications permanent, which suggests notifications should not stay otherwise (/confusion/?) – Benjamin Feb 6 '12 at 16:34

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