In ezpublish.yml in the setting of a group which is set with "legacy_mode: true" you cannot refer to a repository, without getting the following error :

ContextErrorException: Notice: Undefined index: custom_repository in D:\data\ezp-4.2\trunk-2014.03\vendor\ezsystems\ezpublish-kernel\eZ\Bundle\EzPublishCoreBundle\DependencyInjection\EzPublishCoreExtension.php line 417

The only way it will work is if you refer to this repository in a previous group which is not set "legacy_mode: true".