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I've looked at Visual 6502 and it's way beyond me. I've even looked at the scans where it shows how they severed the connection to disable 6502 decimal mode on the NES.

To be fair, the 6502 is very dense, and very hand optimized.

Modern systems tend to use "standard cells" for logic which is a lot more digestible.

The original NMOS 6502 also used a lot of rather weird dynamic logic which can't easily be represented as standard digital logic elements. Some details here:

http://www.aholme.co.uk/6502/Main.htm

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