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I'm using popper mail notification, which integrates into the messaging applet, therefore I have no use for the default message indicator entries. Is there a way to hide/remove them?

I already disabled the thunderbird unity integration add-on.

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up vote 8 down vote accepted

You just need to remove the Thunderbird file from /usr/share/indicators/messages/applications.

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Already tried it, but no luck. – Dinin Oct 15 '11 at 20:04
@Dinin: what steps did you take? Without the addon and the entry in that folder, there should be nothing there. – RolandiXor Oct 15 '11 at 21:12
There was a hidden backup of thunderbird in /usr/share/indicators/messages. Removing this solved my problem. THX – Dinin Oct 19 '11 at 12:35

/usr/share/indicators/messages/applications/ as explained here, are just text files containing path to desktop file. You can blacklist them per-user:

cp /usr/share/indicators/messages/applications/* ~/.config/indicators/messages/applications-blacklist/

enter image description here

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You might need to reload the message indicator app. The following works in xfce (xubuntu)

pkill -HUP -f indicator-messages-service

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