module.config.php

<?php
return array(    
    'doctrine' => array(
        'configuration' => array(
            'orm_default' => array(
                'repository_factory' => 'ServiceLocatorRepositoryFactoryFactory'
            ),
        ),
    ),
);

ServiceLocatorRepositoryFactory.php

<?php


use Doctrine\ORM\EntityManagerInterface;
use Zend\ServiceManager\ServiceLocatorInterface;

class ServiceLocatorRepositoryFactory implements \Doctrine\ORM\Repository\RepositoryFactory
{

    /**
     * @var ServiceLocatorInterface
     */
    private $serviceLocator;

    /**
     * The list of EntityRepository instances.
     *
     * @var \Doctrine\Common\Persistence\ObjectRepository[]
     */
    private $repositoryList = array();

    public function __construct(ServiceLocatorInterface $serviceLocator)
    {
        $this->serviceLocator = $serviceLocator;
    }

    /**
     * {@inheritdoc}
     */
    public function getRepository(EntityManagerInterface $entityManager, $entityName)
    {
        $repositoryHash = $entityManager->getClassMetadata($entityName)->getName() . spl_object_hash($entityManager);
        if (isset($this->repositoryList[$repositoryHash])) {
            return $this->repositoryList[$repositoryHash];
        }
        return $this->repositoryList[$repositoryHash] = $this->createRepository($entityManager, $entityName);
    }

    /**
     * Create a new repository instance for an entity class.
     *
     * @param \Doctrine\ORM\EntityManagerInterface $entityManager The EntityManager instance.
     * @param string                               $entityName    The name of the entity.
     *
     * @return \Doctrine\Common\Persistence\ObjectRepository
     */
    private function createRepository(EntityManagerInterface $entityManager, $entityName)
    {
        /* @var $metadata \Doctrine\ORM\Mapping\ClassMetadata */
        $metadata            = $entityManager->getClassMetadata($entityName);

        if($metadata->customRepositoryClassName && $this->serviceLocator->has($metadata->customRepositoryClassName)) {
            return $this->serviceLocator->get($metadata->customRepositoryClassName);
        }

        $repositoryClassName = $metadata->customRepositoryClassName
            ?: $entityManager->getConfiguration()->getDefaultRepositoryClassName();

        return new $repositoryClassName($entityManager, $metadata);
    }
}

ServiceLocatorRepositoryFactoryFactory.php

<?php


use Zend\ServiceManager\FactoryInterface;
use Zend\ServiceManager\ServiceLocatorInterface;

class ServiceLocatorRepositoryFactoryFactory implements FactoryInterface
{

    /**
     * Create service
     *
     * @param ServiceLocatorInterface $serviceLocator
     * @return mixed
     */
    public function createService(ServiceLocatorInterface $serviceLocator)
    {
        return new ServiceLocatorRepositoryFactory($serviceLocator);
    }
}