cortex: revision graph

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incorporate appendix.2014-03-29, by Robert McIntyre
complete first draft of user guide.2014-03-29, by Robert McIntyre
working on user guide.2014-03-29, by Robert McIntyre
completed first draft.2014-03-29, by Robert McIntyre
completed integration, sleeeeeeppppp.2014-03-29, by Robert McIntyre
s.2014-03-29, by Robert McIntyre
s.2014-03-28, by Robert McIntyre

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