I'm bootstrapping user authentication for phpMyAdmin with WordPress, and probably going to end up hacking the core of phpMyAdmin a bit to get it working properly.
The issue I'm having is that within phpMyAdmin, a few require and require_once expressions use a './path/to/file.php' structure, so the file that I bootstrap phpMyAdmin must be located in the same folder as phpMyAdmin's root.
May I suggest conditionally defining a constant and using it for require expressions?
<?php if ( ! defined( 'PHPMYADMIN_ROOT' ) ) define( 'PHPMYADMIN_ROOT', dirname( __FILE__ ) . '/' ); require( PHPMYADMIN_ROOT . 'path/to/file.php' ); ?>