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CommonSettings.php:

// SiteMatrix hook for 1.16, obsolete in 1.17
$wgHooks['SiteMatrixGetPrivateAndFishbowlWikis'][] = 
'efGetPrivateAndFishbowlWikis';
function efGetPrivateAndFishbowlWikis( &$private, &$fishbowl ) {
    global $IP;
    $private = array_map( 'trim', file( "$IP/../private.dblist" ) );
    $fishbowl = array_map( 'trim', file( "$IP/../fishbowl.dblist" ) );
    return true;
}


and

// Old ones, being obsoleted by the ext above...
#function wfSetupSiteDefaultMessages() {
#    global  $wgMessageCache, $wgSiteDefaultMessages;
#    $wgMessageCache->addMessages( $wgSiteDefaultMessages );
#}
#$wgExtensionFunctions[] = 'wfSetupSiteDefaultMessages';


and

# obsolete - merged
#if( $wmgUseUniversalEditButton ) {
#    include "$IP/extensions/UniversalEditButton/UniversalEditButton.php";
#}

InitialiseSettings.php:

# obsolete, september 2006
#'wgOnlySysopMayMove' => array(
#    'default' => false,
#    'dewiki'  => true, # Report by sansculotte on #mediawiki, TS 2004-10-15
#    'enwiki' => true,
#    'frwiki' => true, # requested by hashar
#    'mediawikiwiki' => true,
#    'commonswiki' => true, # requested by Bdka on #wikimedia-tech, 2006-05-04
#    'enwiktionary' => true, # requested in beer parlour, 13 june 2006
#    'hewiki' => true,
#),

// Obsoleted by WikimediaMessages extension
'wgSiteDefaultMessages' => array(
    'default' => array(
        # Bug 11912
        'sitesupport-url' => 'http://wikimediafoundation.org/wiki/Donate',
        'sitesupport' => 'Donate',
    ),
),



etc etc