I generally just push all my cards together during clean-up and slap them on top of my discard, so it's possible to do it in a non-deliberate way. That said, you are allowed to be deliberate about the top card of your discard. That's all. The order of the rest does not... and should not... and will not, provided you shuffle adequately... matter.
Agreed here. I would say, though, that not only can you be deliberate about the top card (the one "shown" to your opponent), but you are able to be just as deliberate about what remains hidden (the cards in your hand when clean-up begins, as there's no requirement to show those to your opponent). For a simple example: hand starts as Witch-CCCE, play Witch and unluckily draw Witch and C, play 4xC and buy Remodel. Remodel is currently the top card of your discard pile since it was gained before clean up begins. I could put my played cards into the discard pile, then my hand, covering up the Witch with the Estate so you didn't know I burned through both that hand.
Other people in the thread were saying that they moved cards around in their discard because they believed it would result in better hands later. I suppose its fine to do this if you really, really, really, really, really shuffle well. But it's sort of in bad taste, because if you bother ordering your cards in such a way, it implies that you believe that ordering the discard matters, and if you believe ordering the discard matters, it implies you believe your shuffling will be less than adequate.
Lack of good shuffling is the issue, not ordering the discard. But if you order the discard with much deliberation--other than the top card--it suggests a lack of good shuffling is about to occur.
If you are deliberately using your discard order during clean-up to try and give yourself better hands post-shuffle, that's lame. If you have a way of making it work, that's cheating. So we agree there.
But I think we can agree there is at least one legitimate, and legal, reason for manipulating the discarding portion of clean-up: deciding what will show and what will remain hidden to your opponent.