Puzzle dependency charts
So. About puzzle dependency charts...
It's important to map the physical space or layout as much as possible. When playing I notice that games puzzles are always laid out in a way which takes account the most likely path of the player, or their eyes, or their thought processes. They use either statistics/probability, association/conditioning, or rail-roading/fencing.
Another technique is luring / deterring the player. This can be explicit or implicit.
You can do it by hinting, telling, tempting, framing, directing etc., the player in a direction or location, or a way of thinking.
This is a form of reasoning to/with the player, which somewhat creates a dialogue as the player interacts with the game. But it's one-sided really.
I find that composing a scene is infinitely more powerful than just listing its contents.