If you encounter strange problems relating to bookmarks, downloads,
window placement, toolbars, history, or other settings, it is
recommended that you try creating a new profile and attempting to
reproduce the problem before filing bugs.
In order to create a new profile, start Thunderbird with the
-profilemanager switch, e.g. thunderbird -profilemanager

If thunderbird doesn't start at all, first try and remove compreg.dat,
xpti.dat and extensions/Extensions.rdf in your profile-dir, or you
could just delete the old profile-dir,
    rm -r ~/.thunderbird/<profile-dir>
(Be aware that this will delete any locally-stored mail).

To make Thunderbird open links using Firefox, shut down Thunderbird
and add these lines to ~/.thunderbird/<something>.default/prefs.js:

user_pref("network.protocol-handler.app.ftp", "/usr/local/bin/firefox");
user_pref("network.protocol-handler.app.http", "/usr/local/bin/firefox");
user_pref("network.protocol-handler.app.https", "/usr/local/bin/firefox");

