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I have written my Bachelor thesis in org-mode and was incredibly happy with it. There is certainly a difference in requirements for a PhD Thesis, but I cannot think of any missing feature or hard to overcome problem right away.

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What did you use to convert to pdf / html?

org-mode comes with HTML/pdf/DocBook export and you can extend the exporter with your own formats.

Did you find it easy to extend with your own formats? Or to modify an existing format, say html, to produce slightly different output?

I usually use perl/sed/awk + markdown for generating html from my own made-up mini-formats. I'd love to keep the sources in org-mode instead, but I wonder whether elisp is the right language for the type of text munging I want to do.

elisp isn't really good at text munging (that sounds counterintuitive at first, given it is the extension language of an editor) and works much better if your data is structured as s-expressions. AFAIK there used to be project to build a modern parser for org-mode files, but I couldn't tell you how much this has progressed or how usable it is. So, if your export process contains heavy text-munging I'd avoid it.

Modifying the HTML output (adding classes etc.) was fairly OK, I haven't tried anything crazy though.

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