Thunderbird would no longer open links in a web browser. I managed to follow the instructions here to fix the problem:
In Thunderbird go to "Edit --> Preferences --> Advanced" in the Thunderbird menus and click on the "Config Editor" button.
Search for the following three entries:
Set the value of each of these three entries to true (you can do this by double-clicking on each entry)
I have no idea why it is so obscure.
Another problem I had was that Ctrl-Alt-Del would now reboot instead of shutting down. I had executed the script in the upgrade instructions to use all the new configuration files. I fixed the problem by using the old configuration file:
bash #diff inittab inittab.bak
< ca::ctrlaltdel:/sbin/shutdown -t5 -r now
> ca::ctrlaltdel:/sbin/shutdown -t5 -h now
bash #mv inittab.bak inittab