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In my current project I use three different markdown inspired formats.
I am currently working on a parser generator oalex that uses some Markdown-inspired components. I was planning to use headers and module boundaries. While I have the code to parse it, I haven't developed modules yet. It also uses indented code blocks to represent input patterns in rules and sample input in unit tests.
First you should be using a disambiguous version of Markdown such as CommonMark.
I'm using some custom formatting in one of my formats, but it's not exactly like in markdown: