[TASK] Properly deprecate direct access to DB and file list

Change-Id: I5ab30c14c57e0dc777d6faadc48fb762572c1469
Reviewed-on: http://review.typo3.org/3821
Reviewed-by: Philipp Gampe
Reviewed-by: Georg Ringer
Tested-by: Georg Ringer
Reviewed-by: Xavier Perseguers
Tested-by: Xavier Perseguers