Since it’s been asked on occasion how I write the thesis, first here is a screenshot:
And here are some statistics about my PhD dissertation writing tools.
Text editor: Scrivener (primarily)
Both Swiss-Army Knife and grand masterplan-style organizational tool, Scrivener is mostly useful for organizing/reorganizing the thesis into multiple sections and sub-sections, in any whichever way. It has a ton of other features I barely use, and probably should have—word count limit-counters, status indicators, etc.
Unlike most people who use WYSIWYG editors like MS Word to format their docs/theses, I don’t use Scrivener for this. Instead I write in a markup language (e.g. HTML)—namely Markdown—and then use a Latex template to format in PDF as desired. (See more below.)
Sometimes for quick and dirty documents (like presentation handouts/etc.), I use Apple’s Pages—necessary evil, I know. Sometimes I use just a basic text editor when writing Markdown, like Sublime Text.
Otherwise I use the following while editing in Scrivener:
Since my last Master’s thesis, I have ultimately used LaTeX to format my work. There are many good reasons to use Latex, once you’ve taken the time and 2 weeks (in my case) to figure it out. For more persuasion and recommendation, esp. ancient philosophy people, see Willie Costello’s excellent guide and persuasion.
However writing in Latex can become quite cumbersome, in my experience. So for the PhD thesis and most writing, I have used Markdown—which is very lightweight by comparison. I then export the document from Scrivener as-is, no formatting additions, and then use Pandoc to convert the Markdown doc to Latex—ultimately to PDF.
Pandoc is great for converting your Markdown doc (or theoretically any other markup language) into other formats than Latex/PDF, like (especially!) MS Word, HTML, etc. So the usefulness for using Pandoc expands beyond convenience with using Markdown.
As anyone who’s written any kind of thesis knows, bibliography and citations are a b***—without a reference manager(!!). So for anything that isn’t an ancient primary source-citation (I usually just cite directly, rather than typical @DAncona1991-style citations), I have ended up using Bookends. For my purposes, they have an incredible amount of customizability (like Scrivener)—and one reason this has beat out other ref. managers (e.g. Papers 3).
Otherwise for free, open-source workable alternatives, Zotero is excellent. The only reason I ended up with Bookends was the extra options it gives you, esp. for Bibtex.
And Bibtex (sometimes using Biber)—since Latex (and Pandoc) use the format for citations. So I export my references from Bookends in a Bibtex file, and then use when I run Pandoc in Terminal.
Recommendations for Improvement?
So far this system is definitely not fixed—there is certainly room for improvement. For instance, a number of things could be scripted and maybe put in a GUI, like an Apple Automator script (e.g., automating the Pandoc process on exporting from Scrivener, rather than opening Terminal and running Pandoc separately). I may also switch back to Zotero at some point—if pain isn’t involved.
Otherwise any advice/feedback, let me know!