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This change separates the master box from the root box, as the single master copy of boxes. Before this change, the root box is the source of copies, and also it runs builtin classes' code. Builtin code makes changes by requiring files, thus the source of copies is mutable, be different from the past one. This causes different internal states of boxes, depending on when it is created. After this change, all boxes are created from the master box, and the master box never runs code, so it realizes the immutable source of copies. This also makes is possible to separate RubyGems (and other default gems) from each boxes. All boxes will have their own copies of RubyGems. RubyGems has its internal state, but it'll be separated between boxes after this change.