definitely killed by rocks, Madara was.He looked under a lot of rocks.
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On topic, who knows? Tobi knows. I'm willing to bet that Kabuto's response to Tobi ("Oh, you know...") was mean literally and not just as a dismissive "oh, you know." Kabuto is a sarcastic bast***, and he was really saying "don't play stupid, you know exactly how I did this." In other words, Tobi knows the circumstances behind Madara's death, or at least knows where the remains were located -- Tobi probably disposed of or hid the remains himself. That entire conversation is full of subtle, contextual hinds, like how Kabuto commends Madara and Tobi calls him a "wise guy" or "smartass" because Kabuto was talking to the Madara in the coffin and not the person who claimed to be Madara moments earlier.