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Big beautiful refactoring #386

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See #385

… updated $ref syntax (matching certificates).
…if a different design was passed to it which seems bizzare since it goes out of its way to support having a different type for different designs. So, I modified it to work like the type cache in ast and do what I think it wanted to do in the first place.
…ke it clearer the return type since I found bugs in the code related to this.
…n't have (i.e. in @config). Also true for implemented and prohibited.
…ns, CSRs, and traps that aren't in the configuration). Still need to fix traps and interrupts.
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