$wgConf->settings = [

# ...

# '+' triggers a merge with this and the value of $wgGroupPermissions defined
#  in DefaultSettings.php
'+wgGroupPermissions' => [

    # Allow bureaucrats to change status on remote wikis
    # and allow anonymous users to create pages (this part
    # will not be merged with 'default' since there are no
    # "+" in front of 'centralwiki')
    'centralwiki' => [
        'bureaucrat' => [
            'userrights-interwiki' => true,
        ],
    ],

    # A wiki with rollback right given to logged-in users
    # the 'default' part will be merged with this value
    # (i.e., anonymous users won't be able to create pages)
    '+somewiki' => [
        'user' => [
            'rollback' => true,
        ],
    ],

    # Disallow anonymous users to create pages.
    # Note: the 'default' key should never have a "+" in front of it
    'default' => [
        '*' => [
            'createpage' => false,
            'createtalk' => false,
        ],
    ],
],

# ...

];

$wgConf->settings = [
'wgConfigurationSetting' => [
    'default' => 'defaultvalue',
    'wikidatabasename1' => 'value that overrides default for this wiki',
],
# To merge the settings you set here with those in DefaultSettings.php:
'+wgConfigurationSetting' => [
# Note: This and DefaultSettings.php are NOT the same! The default specified here
#       overrides that in DefaultSettings.php and becomes the new default for all
#       your wikis unless you choose to override it for a particular wiki,
#       like for wikidatabasename1 here.
    'default' => 'defaultvalue',
    'wikidatabasename1' => 'value that overrides default for this wiki',
],
];

<?php

$wgConf->settings = [

'wgServer' => [
    # If you want to allow the usage of https, use '//localhost'
    #  and set 'http://localhost' at 'wgCanonicalServer'
    'default' => 'http://localhost',
],

'wgCanonicalServer' => [
    'default' => 'http://localhost',
],

'wgScriptPath' => [
    'default' => '/$wiki',
],

'wgArticlePath' => [
    'default' => '/$wiki/index.php/$1',
],

'wgSitename' => [
    'default' => 'Wikipedia',
    'frwiki' => 'Wikipédia', # accent in French
],

'wgLanguageCode' => [
    'default' => '$lang',
],

'wgLocalInterwiki' => [
    'default' => '$lang',
],

];

$wgLocalDatabases = [
    'dewiki',
    'enwiki',
    'frwiki',
];

$wgConf->wikis = $wgLocalDatabases;
$wgConf->suffixes = [ 'wiki' ];
$wgConf->localVHosts = [ 'localhost' ];

require_once "$IP/InitialiseSettings.php";

function efGetSiteParams( $conf, $wiki ) {
    $site = null;
    $lang = null;
    foreach( $conf->suffixes as $suffix ) {
        if ( substr( $wiki, -strlen( $suffix ) ) === $suffix ) {
            $site = $suffix;
            $lang = substr( $wiki, 0, -strlen( $suffix ) );
            break;
        }
    }
    return [
        'suffix' => $site,
        'lang' => $lang,
        'params' => [
            'lang' => $lang,
            'site' => $site,
            'wiki' => $wiki,
        ],
        'tags' => [],
    ];
}

$wgConf->suffixes = $wgLocalDatabases;
$wgConf->siteParamsCallback = 'efGetSiteParams';
$wgConf->extractAllGlobals( $wgDBname );