Chapter 7 and 8

In chapter 7 and 8, many surprising things were revealed. The reader finds out what happened to Jem that frightened him so much, there are still items placed in the tree hole (until it gets filled with cement), Mrs. Radley died and Mrs. Maude's house catches on fire. These are all important. What I don't understand is why was Jem so frightened that his pants were fixed when he knew in the back of his mind Boo was probably alive? My suspicion of Boo being alive was confirmed, I believe he's the one leaving the gifts for the kids. Why did he help mrs Maudie? Why was the tree hole filled? I believe Boo is not all bad but does have a dark side. I predict that he will look out for the kids through everything; he has a strong emotional attachment to them.