Oh these are great, and I hadn't known of markdeep. Thank you!
FWIW, my toolchain is currently markdown files in folders. I pre-pend 000-format numbers to file/dir names so they're assorted by ls or tree. Rendering is a bash script that runs pp first, since files include others using !include(), producing a single .md in /tmp. The mighty pandoc of course, to produce a Word doc, which is then the basis for all further rendering. HTML and plaintext are generated from that with pandoc. I was using pandoc to produce PDFs, but switched to calling libreoffice headless to generate PDF from the Word doc, since this seems to match formatting most closely.
Sounds fussy, but it's a few lines of bash, fairly reliable and reasonably rapid.
One outstanding issue is tables. The Word doc always requires reformatting tables for column width, flow, etc. I can't seem to get pandoc to carry the styles effectively from a custom reference.docx file. I'm looking at ways to render tables separately, format by hand, then include them into the main doc later.