I wanted to have phpmyadmin save some of my settings in order to improve the UI and enable the advanced features like query history. Changing the UI settings was easy enough – you can use the setup routine to create the settings and/or grab and uncomment from the sample config. If you use setup, just remember to hit “save” before clicking on a new config group (oops).
For the advanced features, however, I had a bit of a hard time to get rid of the “The additional features for working with linked tables have been deactivated…” error. I started over and it turned out to be pretty simple. Here are the steps that worked for me:
You should be good-to-go.
Note if you are having trouble with a version installed/updated via a software package manager (like Yum — Remi usually has the latest, which is nice), the config file it resources may be in /etc/phpMyAdmin/config.inc.php — something that also was tripping me up.