something like pandoc -t pdf --template=https://github.com/Wandmalfarbe/pandoc-latex-template/blob/master/eisvogel.tex main.md chap1.md chap2.md chap3.md -o paper.pdf should work out of the box ... if you really want "includes", check out this Lua filter for Pandoc: https://github.com/pandoc/lua-filters/tree/master/include-files


I found, that the easiest way of merging multiple markdown files together is just by grabbing them with glob like this:

pandoc src/*.md -o paper.pdf



