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From @boneskull:
@psq I'm not really understanding the use case of jsdox against anything but very small codebases. If you have one file, you can generate a README.md from it (sort of; the file won't be named README.md and it won't go where you want, but that's another open issue). If you have multiple files, you get a directory (or directory hierarchy) full of Markdown files.
Is the user to browse them individually? They don't make a web site. They can't be used with Jekyll because they have no Front Matter. You could potentially create an entire GitHub wiki out of the non-hierarchical files (using -r; not -rr), but a wiki is not really suitable for API documentation. Does some other converter consume them and turn them into a PDF?
I've only used jsdox for a very small module or two b/c of its limitations. If it generated a Jekyll site (and had more tag support, of course), then it's a viable alternative to jsdoc itself.