implementing solution using <ifModule mod_authz_core>

lib/private/setup.php

@@ -168,10 +168,14 @@ class OC_Setup {
 		//Require all denied
 		$now =  date('Y-m-d H:i:s');
 		$content = "# Generated by ownCloud on $now\n";
-		$content.= "# line below if for Apache 2.4 - please uncomment if you run Apache 2.4\n";
-		$content.= "# Require all denied\n\n";
-		$content.= "# line below if for Apache 2.2 - please remove it once you upgrade to Apache 2.4\n";
-		$content.= "deny from all\n\n";
+		$content.= "# line below if for Apache 2.4\n";
+		$content.= "<ifModule mod_authz_core>\n";
+		$content.= "Require all denied\n";
+		$content.= "</ifModule>\n\n";
+		$content.= "# line below if for Apache 2.2\n";
+		$content.= "<ifModule !mod_authz_core>\n";
+		$content.= "deny from all\n";
+		$content.= "</ifModule>\n\n";
 		$content.= "# section for Apache 2.2 and 2.4\n";
 		$content.= "IndexIgnore *\n";
 		file_put_contents(OC_Config::getValue('datadirectory', OC::$SERVERROOT.'/data').'/.htaccess', $content);