Shell wrappers, of course! I ran a couple of them yesterday with the help flag, saw exactly the same message generated by the multimarkdown binary and concluded incorrectly they were binary wrappers . See, not my specialty.
Back to your generate_user_manual.rb script, I see that one of its functions is:
Some of the symbols listed are in the compilation Replacements and others, like the arrow symbols, are not. Is it possible that Replacements misses?
I have another question about MutiMarkdown and Pandoc, but is way more generic and so I decided to make a new post here.