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Switching to Github Flavoured Markdown results in a LOT of differences between rendering. The bulk of these are related to blank lines in HTML blocks, which fall foul of rules 6 and 7 of HTML blocks in GFM (see: https://github.github.com/gfm/#html-blocks), and cause rendering errors. We can (painstakingly) remove all these blank lines to produce a compiled output that only differs in desirable ways. This is mostly fine, but it does mean that there are now no empty lines in code samples, which may or may not be a blocker.
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