Normally, upgrading is just a matter of installing the newer version into a separate directory and copying the previous version's config.inc.php to the new directory. If the previous version is phpMyAdmin 2.6.0 or older, we cannot copy its config.inc.php to the new version because the file format has changed too much.
Note
An upgrade—or first-installation—path that should not be taken is to copy libraries/config.default.php to config.inc.php, since this default configuration file is version-specific and is not guaranteed to work for future versions.
New parameters appear from version to version. They are documented in Documentation.html and defined in libraries/config.default.php. If a configuration parameter is not present in config.inc.php, its value from libraries/config.default.php will be used; so we do not have to include it into config.inc.php if the default value suits us.
Special care must be taken to propagate the changes we might have made to the layout.inc...