When you run out of cards in your deck, I assume that you shuffle in your discard pile at that point. Not sure about genric shuffling your deck.
If you encounter a mechanic that makes you shuffle your deck, do you shuffle in your discard pile?
Why would you assume that?
The answer is no - to both questions. You do NOT shuffle your discard pile into your deck, unless a card action text specifically were to tell you to do so.
If you run out of cards in your deck, you just can't draw. Unlike some other card games, the game isn't over if you run out either.