> Someone, possibly MetalliC, should explain how this Actel FPGA
> functions to get a better understanding to hook Area 51 Site 4's inputs.
That's the thing though, the use of an FPGA in any given circuit is unique to that circuit.
The bitstream that configures its macrocells is ultimately what determines how it functions in a given application. FPGAs are only very rarely emulated on a bitstream level, though, they're typically black-boxed based on what the particular application-specific functionality does.
The end result of this is that knowing how it works in Sega's particular application doesn't help figure out how it works in, say, Atari's application of it. The underlying functionality could be, and most likely is, entirely different.
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