[GH-392] Replaced a shallow-copy with a deep-copy to avoid side effects.

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

Url: https://github.com/doctrine/doctrine2/pull/392

Message:

Hey!

I'm currently using Symfony 2.1 + Doctrine master branch + Pager fanta master branch.

I'm facing a very vicious issue.

The doctrine paginator is able to clone a query with his `cloneQuery` method. This method will only clone the query without this parameters & hints. The issue is the parameters is setted with the `setParameters` method which will only affect the ArrayCollection reference to the new query builder and so, shared the reference between the two queries.

This PR will make a deep-copy of the ArrayCollection instead of a simple shallow-copy.

I'm not sure if this fix is the best solution.

Let me know if you need more information.