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I couldn't find where I can change Gnome Shell notification settings. I clicked the button that appears with "Don't Show Again" (or something like that) label on a notification, and now when that notification appears, it never disappears until I click on that.

Where is the configuration window of Gnome Shell notifications?

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There is no way to easily configure gnome-shell notifications as of yet. You can disable them or configure them to time out.

dconf-editor allows you to configure some settings

sudo apt-get install dconf-editor
dconf-editor

You can also modify notify-send so the messages are transient.

# Move the current script to a backup location
sudo mv /usr/bin/notify-send /usr/bin/notify-send.bak

Now, use gedit for a new wrapper script

gksu gedit /usr/bin/notify-send

copy-paste this into that file

#!/bin/bash
/usr/bin/notify-send --hint int:transient:1 "$@"

Save the script , exit gedit, and make it executable

sudo chmod a+x /usr/bin/notify-send

See also this forums post for addition suggestions.

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Are you sure your answer will work as intended? /usr/bin/notify-send --hint int:transient:1 "$@" will call /usr/bin/notify-send which contains /usr/bin/notify-send --hint int:transient:1 "$@", you will fall into a recursive script with no end. usr/bin/notify-send should contain /usr/bin/notify-send.bak --hint int:transient:1 "$@", no? –  danjjl May 7 '12 at 15:36
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