Specifically: there's now just the one .h file at the top level, giving a clear indication of what a user should read. That separates implementation from interface. It also devolves a lot more to the base class because doing so makes debug builds less of a hassle. The all-RAM 6502 has been shuffled off into a subfolder, to indicate that it's not something you necessarily need know about. Also general documentation improvements have been applied: incorrect citing of the recurring-template pattern has been removed and the meaning of the two BusHandler methods has now accrued at the bus handler.
