Comment 4 for bug 939258

I still have this problem with indicator-messages 0.5.4.94-0ubuntu1:

tjgq@velma:~$ aptitude show indicator-messages | grep Version
Version: 0.5.94-0ubuntu1
tjgq@velma:~$ ls -l .config/indicators/messages/applications-blacklist/
total 4
lrwxrwxrwx 1 tjgq tjgq 55 Mar 21 23:40 thunderbird -> /usr/share/indicators/messages/applications/thunderbird
lrwxrwxrwx 1 tjgq tjgq 67 Mar 23 00:32 ubuntuone-control-panel -> /usr/share/indicators/messages/applications/ubuntuone-control-panel
lrwxrwxrwx 1 tjgq tjgq 49 Mar 23 00:36 xchat -> /usr/share/indicators/messages/applications/xchat

Yet Thunderbird, Ubuntu One and Xchat all appear in the indicator.