I have been writing my thesis as an org-mode file in git that is automatically published [0] as a pdf every time I commit using a bash script tangled as a commit hook. Figures are (or can be) computed from live data, and org-ref can automatically manage and format all my references as I go without the insanity inducing workflows that one usually has to resort to. Another amazing thing about org-mode is that I can write a code block to hit a remote api (e.g. google docs) and fill and format entire chapters from a collaborative editing source that my advisor is comfortable using, C-c C-c and it is embedded in the document. Perfect for stitching papers together from a variety of sources.<p>While there is a learning curve, the peace of mind of having a single tool that enables me to use any tool I need to use was such a relief after years of other painful writing and publishing workflows.<p>If you are starting a PhD today and are going to do anything at all with code, I seriously suggest you learn org-mode. By the time you finish, not only will you have a PhD, but even if you don't you will have the power of one of the most amazing authoring tools under your command! (I would say, "Learn org-mode, simplify your life!" but emacs tends to lead to other complications).<p>0. <a href="https://orgmode.org/manual/Publishing.html" rel="nofollow">https://orgmode.org/manual/Publishing.html</a>
Could be be done, but does not feel like the appropriate tool. Org mode translates to a basic latex only, that is a huge waste of TeX power.<p>I did my thesis entirely in LaTeX, so I have some experience in the theme, and it was a rollercoaster. There is always some really special table, graph, arrangement, extra space needs, that you can do only programming with the real stuff. Doing the same with org mode would have been stuff of nightmares (even if org tex has some nice qualities that LaTex does not have, like fast shrinkable text).<p>I missed only a thing. Being able to do in situ calculus in LaTeX (filling columns and totals in tables excel style), but is not really the right tool for that so you can't blame TeX for that. The team of R+Latex filled the gape nicely.<p>Apart of this, TeX environment has planned and build yet anything that you could dream when you write a PHD thesis. From basic, to really esotheric. Can be difficult sometimes, but is awesome.
Back in the late 2000's I looked around for the right tool for my Ph.D. dissertation and quickly ruled out Word, Libre (or Open Office) Writer, or any wysiwyg tool, because they 1) lacked fast, easy ways to work at the structural (tree) level of the document, which is important when you have many sections and subsections to organize thoughts and arguments; 2) couldn't do mathematical notation well; 3) didn't integrate well with the reference management tool I was using then, Mendeley.<p>As an Emacs lover, I soon found Org, and it was (and remains) the perfect tool, for working in plain text — which will never be obsolete, and works easily with git or version control. Then and now, nothing could match Org speed and flexibility: structural editing (creating nodes, moving nodes, promote/out-dent a node, demote/in-dent a node) was and is fundamental to Org (unlike Markdown etc), and it's ridiculously easy to reorganize thinking and writing as you go. You can export to LaTeX (or HTML) and customize formatting as needed, while also including code blocks from multiple languages. Integration with BibTeX was tight, and made handling hundreds of references easy.<p>Where other writing tools for complex documents previously made me cringe and cuss, Org makes writing a pure joy, freeing the mind to work entirely on content and its structure.
I'm not sure about other fields, but most theses in computer science these days are usually a stitch-up of your papers + some glue text/backstory. I.e. 80% of your thesis is already in LaTeX format. Org Mode only adds complexity to your workflow.