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I crated a new version of the specification for HexJSON. This version includes semantic version numbering and a more complete layout description. Using these additions the layout of the map should be unambiguous. I am proposing this extension as a precursor to modifications to the relevant code in d3-hexJSON and hexmaps. Feel free to comment on this proposal.
I created a different branch given the possible impact. However, since this is my first pull request ever it's highly likely that isnt done completely right :). So if you want this done in another way please contact me. My mailadres is on my website.