[GH-376] De-deprecate transaction handling methods

This issue is created automatically through a Github pull request on behalf of lstrojny:

Url: https://github.com/doctrine/doctrine2/pull/376

Message:

As discussed with @beberlei over IRC, deprecating transaction handling methods make the API cleaner but testing of Entity Manager dependent components much messier. Also suggesting to use `$em->getConnection()->beginTransaction()` feels like a violation of the law of demeter.

Therefore this pull request would remove the deprecation warnings from `EntityManager::beginTransaction()`, `EntityManager::commit()`, `EntityManager::rollback()`.