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You can start by checking out the "zerocoin" branch of
https://github.com/Anoncoin/anoncoin and looking in src/libzerocoin . Try reading Tutorial.cpp to get an overall feel for how zerocoin works, then move on to understanding the rest of it. Most of that code was not written by me, by the way.
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Curious, who wrote most of the zerocoin code? I would imagine only a handful of programmers in this world have the right knowledge and skills to implement the zerocoin algorithm.