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Re:Don’t Use Markdown for Documentation by _getify on Wednesday March 16, 2016 @12:42PM (#11298661)
The books were intended as source material for publishing, so I didn't embed any crosslinks in the documents.

However, I always use markdown for all my OSS project documentation (READMEs, etc), and I do lots and lots of cross-referencing in that context. I use simple markdown links to named-section anchors.

It's a tiny bit more manual than I'd like, but it's never stopped me from doing technical documentation effectively.

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