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Purification needs extensive documentation
We need a separate .md doc for how to configure purification. It should tie together the code, circuit diagrams and text in kaaki's thesis, and research references.
This should include extensive diagrams, which, with permission, could come from kaaki's thesis.
Related to the need to rewrite the code that generates purification rules, #104.
Okay, what I have done here is extensively comment the code itself, using doxygen. I have included two figures from kaaki's PRA. Some of the other cases still need the figures. Someone should step up and add the additional figures. There is no need to do figures for the last (default) case. There is no need to put the same figure in more than once.
I don't think we're quite done with this, but close...can we finish this off? Unpinning it as an issue.