The Stone is probably there because Quirrel covered how he led Flamel to believe the Stone had to be actually in the trap before it would work; ch108:
"Did you bluff everyone into believing you had some way of finding the Stone?" Harry said aloud. "So that Perenelle would put it inside Hogwarts, where Dumbledore could guard it?"
The Defense Professor sighed, not looking up from the cauldron. "I suppose that strategem would be futile to conceal from you. Yes, after I possessed Quirrell and returned, I implemented a strategy I had conceived while gazing at the stars. First I made sure to be accepted as Defense Professor at Hogwarts, for it would not do to have suspicions raised while I was still seeking employment. When that was done, I arranged for one of Perenelle's curse-breaking expeditions to discover a falsified but credible inscription describing how the Crown of the Serpent could be used to seek out the Stone wherever it was hidden. Immediately after, before Perenelle could buy up the Crown, it was stolen; furthermore I left clear indications that the thief had possessed the power to speak to snakes. So Perenelle thought that I could infallibly find the Stone's location, and that it needed a guardian powerful enough to defeat me. That is how the Stone came to be held in Hogwarts, in Dumbledore's domain. Just as I intended, naturally, since I had already gained access to Hogwarts for the year. I think that is all of this that concerns you, if I speak not of future plans."
He arranged for the Stone to be in Hogwarts. Whether it's at the end of that particular series of traps is not entirely certain. I'm sure someone like Moody would point out the flaws inherent in a system that students can penetrate. Why not just stick it in the Room of Requirement or some hidden room that only the Headmaster can access (and use proper security)?
New long chapter! Since I expect its discussion to generate more than 160 comments (which would push the previous thread over the 500 comment limit) before the next chapter is posted, here is a new thread.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 108
(and chapter 109, once it comes out on Monday).EDIT: There have now been two separate calls for having one thread per chapter, along with a poll in this thread. If the poll in this thread indicates a majority preference for one thread per chapter by Monday, I will edit this post to make it for chapter 108 only. In that case a new thread for chapter 109 should be posted by whoever gets a chance and wants to after the chapter is released.
EDIT 2: The poll indicates a large majority (currently 78%) in favor of one thread per chapter. This post has been edited accordingly.
There is a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: