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pandoc
Pandoc is a powerful command line tool available for all operating systems that transcribes text from one type of document to another. It is used behind the scenes by the R package rmarkdown to translate markdown to latex and then translates the latex file to a resulting html or pdf file. Thus, pandoc is an integral part of creating a 508 compliant document. This help page is hyper-focused on the options within pandoc that facilitate 508 compliance, i.e., tagging. Here, we are focused on how tagged pdf documents are generated using templates within the sa4ss R package. For full documentation of pandoc see the user manual.
Raw TeX is allowed to preserve the richest formatting as possible and if you desire to keep this formatting specified in the original file, then one would would to allow raw. However, when converting to formats like docx you cannot use raw TeX or HTML. Therefore, one must think deeply about what you want to keep as raw and if you want to turn this functionality off. raw_tex allows raw LaTeX, TeX, and ConTeXt in the document. This extension can be enabled/disabled for many formats, including markdown.