LaTeX to Markdown

Expect a good draft, not a finished document. Pandoc's LaTeX reader knows the common commands and many standard packages, but a macro it does not recognise is dropped or carried through as raw LaTeX. Custom class files change nothing here, because only the text of the single file you drop is passed to pandoc. Read the output and fix the handful of places that came through as raw commands.

Because only the one file you drop reaches pandoc; nothing on this page can open the other files an input or include line names. Flatten the project into a single .tex first, by pasting the chapters together or running a flattening tool locally, then convert that.

Citation commands are not turned into formatted references. Pandoc's citation processor is not enabled here and your .bib file is not available to it either, so cite commands come through as citations rather than as rendered text. Any complaint pandoc has about an unresolved citation appears as a console warning prefixed with "pandoc:".

Yes. Pandoc keeps math as math, writing it into the Markdown between dollar signs for inline formulas and double dollar signs for display ones. Renderers such as MathJax and KaTeX read that directly, so the equations stay equations rather than becoming garbled text.

An includegraphics command becomes a Markdown image link carrying the same path. The image file itself is never read, so keep the pictures alongside the Markdown at those paths. Figure environments become images with their captions where pandoc can match them up.

Use Markdown to LaTeX. It writes a document body rather than a compilable file, with no documentclass line or preamble, which is the counterpart of what happens here: your preamble is exactly the part that has no Markdown equivalent and is lost on the way in.