.. How are these hints organized?

There are no time constraints in this game -- that is, no time seems to pass, you never sleep, and there are no new days to mark the passage of time. So I've arranged the hints according to the major goals in the game; these are more or less the same goals listed in the Master player's task list, but with different titles so as not to give too much away. Some puzzles can occur in different places, depending on the order in which you personally explore. If you can't find a puzzle where you think it should be, check the Puzzles section, where there are links to all the puzzles in the game.