Configure $wgConfigureAdditionalExtensions
Fragment of a discussion from User talk:IAlex
The first part is correct. You need to define your extension in $wgConfigureAdditionalExtensions after including the Configure extension itself but before calling efConfigureSetup() since the inclusion of the extensions sets that variable to an empty array (to prevent register globals vulnerability) and it will be used in efConfigureSetup(). The best way to do this is to put it directly in LocalSettings.php between the two statements described just above.