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Not sure Google would be able to index the docs, since they are in markdown format. But I'm not an expert in how Google index the pages.

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No, google doesn't. I've built a similar solution for the Cocos2D documentation that is going to be released soon. I've added a php server component to deliver HTML snapshots to google crawlers for that purpose.

I have now released my similar documentation system that supports SEO: https://github.com/Ben-G/Lightdoc

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