When playing our first game last night, we got stuck trying to figure out what to do when one's deck runs out. We decided to shuffle the discard pile and insert it under the on-deck card as a fresh deck, because that's the only thing that makes sense. It is weird that the rulebook does not cover this.
If you go to flip your on-deck cards and can't, you shuffle your discards and make a new deck from them. This is common for most deck-building type games. The rulebook explains this in "How to Play" under "Planting Phase" (pg. 8): "Whenever your deck is empty and you need to reveal a new on-deck card, shuffle your discard pile, it becomes your draw deck. If all of your cards are in your field, then you must pass."