This resides in the nebulous region between canon and headcanon, so hear me out. Watson used to have no idea how Holmes organised anything. Holmes used to get really upset about anything being moved, even if it is in a pile in the corner of a room (especially then). He wouldn't let Mrs Hudson clean. That's why Watson sometimes asks Holmes to clean things up. He would do it himself, but has no idea where he would keep things. And Holmes hates putting things away, because in ADHD, Out of Sight= Out of Mind. After Holmes comes back from the dead though, he finds that everything had been organised. (Maybe Mycroft did it. Maybe it was Mrs Hudson.) And when Watson sees this, he just absentmindedly starts putting them back where they used to be BEFORE. And Holmes, being Holmes, recognises it. After the events of Empty House, Holmes and Watson sit on the floor in 221B with everything scattered around them as Holmes tells Watson about his previous cases. And Watson still doesn't understand how Holmes organises anything, but he memorises the setup anyway.