Ready for a brand new workflow! Where do I start?

Correct, this is mostly one-way street with a few exceptions. There are some tweaks if you go the MMD/Pandoc route, like you can add a unique ID to each markdown section so you know which file in the binder it came from if e.g. the title changes.

Personally I never really need to round-trip markdown text (what is your use-case?) BUT if I could have my perfect “simplified” Scrivener, I would ditch Apple’s legacy RTF editor component, and have the Scrivener editor style markdown live. The compiler would use Pandoc for all output formatting. I would then have the power of the Binder / outliner (I never use the corkboard), plus the flexibility of plain-text and the superpowers of the compiler. But I am very doubtful that KB will ditch RTF, and it would be really a tough cookie for KB to modify RTF to support such a flexible conversion (he did make a “simple” RTF<->Markdown convertor, but as you can see it is quite limited)…

Have you tried Ulysses? e.g. leolabs.org/blog/thesis-in-markdown

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