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I got it to work with .md files (instead of .html) by changing "content" to "page.content", which uses the un-parsed text. This is more in line with a typical Jekyll workflow.
Updated Using with Jekyll (markdown)
I imagine that I am not the only one interested in hosting remark files from within my github pages site and, after spending an evening finding the solution, I figured that this may deserve to be in the wiki.
fixed GFM screwup
spaces at beginning of first line of injected content break properties on first slide (tested on Jekyll 3.1.3)
Add jekyll link
Created Using with Jekyll (markdown)