How familiar are you with the permission scheme of Linux?
Basically, a person who has "root" can do anything on the system. A person who does not - cannot. Thunderbird should be installed as root, yes - but don't run it as root. When you run it as a regular user, it will create a hidden ".thunderbird" folder in your home folder - which will store all your prsonalized settings, data, and emails, etc. Also - what distro are you using? If you're using Debian (or Ubuntu), PCLinuxOS, or another popular distro - you may be able to install Thunderbird just by doing sudo apt-get install mozilla-thunderbird
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