Markdown is a really nice format. It's clean, easy to learn, and can be outputted to formats like PDF, Docx, and Latex with the help of John MacFarlane's Pandoc. I decided to write my PhD thesis in Markdown after being inspired by a colleague (thanks again Steve!).
It was a really enjoyable way to work, so I'm sharing the template in case anyone would like to reuse it. The style is based around guidelines for University College London, but could easily be adapted: https://github.com/tompollard/phd_thesis_markdown
There are comments.
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