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Have you tried Pandoc[0]? It's the best, simplest solution I've been able to find for writing content in Markdown, and then almost trivially exporting that same content into PDF manuscripts, or PDF presentations, or HTML presentations, or more, without having to change the source content. It seems to be increasingly popular in academia for handling class notes/slides/papers all in one go. It can have good citation processing with cite-proc [1]. One of my favorite things about it is, if you know you're just going to be exporting to a specific filetype like HTML or LaTeX, you can just plain throw in code for that language directly into the Markdown, and Pandoc will run/include it.

(shameless plug alert) I wrote a super-simple Makefile script for using Pandoc, called acadoc [2]. It lets you call "make beamer", "make manuscript", "make html_presentation", etc., in a directory with Markdown files to turn them all into whatever presentation/manuscript/paper/etc. you want. The key thing, though, is that for LaTeX presentations/etc. it uses an intermediary "style/manuscript.tex" file to customize how you want your resulting LaTeX to look -- so if you want the same content, but decide the presentation looks better with white-on-black instead of black-on-white, you only need make a few changes and create a "style/manuscript_dark.tex", copy-paste that style in the Makefile, and now you can call "make manuscript_dark". It's meant to be quick and easy to use, and theoretically easy to add new recipes to.

If you want some more serious power about multiple document-type exporting, check out the links in the Acknowledgements section of Acadoc, shown here:

- https://kieranhealy.org/blog/archives/2014/01/23/plain-text/ - http://jeromyanglim.blogspot.com/2012/07/beamer-pandoc-markd... - https://github.com/timtylin/scholdoc - http://scholarlymarkdown.com/

(Yes, I know LaTeX styles/stylesheets are a thing, but I've never taken the time to learn them, nor figure out if they can do all the custom formatting a regular .tex stylization file can do.)

[0] http://pandoc.org/

[1] https://github.com/jgm/pandoc-citeproc

[2] https://github.com/asoplata/acadoc




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