Any special folder/naming conventions for the md files?

Example:
2.0/cas_protocol_2_0.md
3.0/cas_protocol_3_0.md

Seems reasonable. At first I thought subdirectories seemed overkill, but your point about images or other resources for rendering the markup seems valid. I will say that the most likely use case will be linking to the markdown file contents on GitHub, where it should be rendered properly. Not sure how resources/formatting would work in that case at all. GitHub-flavored markdown doesn't allow too much formatting in my experience.

M

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