I’ve ended up going back to Scrivener for my doctoral thesis. There are a few reasons why:

• most importantly, I realised that I did my best writing in Scrivener. I wrote my undergraduate dissertation in Scrivener, and I was able to publish it in an A-ranked peer-reviewed journal. The main thing I notice going back and reading that article is that my progression of thought and argument was clear. Scrivener doesn’t make it easy to write, but it does make it easy to organise the ideas in a long piece of writing.
• one aspect of this is its outlining tool. For my masters writing, I used a separate outliner. A specialised tool is always easier and better, but the problem is that the writing and the outline are never in sync with each other, because as I write my idea of the outline changes. Scrivener’s builtin outliner is very good, not as good as a specialised tool but still excellent — and because the outliner, synopsis, and notes tools are attached to the sections in the document hierarchy, they never get divorced from the actual thesis.
• version 3 of Scrivener introduces excellent support for Markdown and other markup-based formats, by allowing the conversion of its styles to markup. This is a game-changer for my use (processing via Pandoc).

The real test will come in a few weeks when I submit my first major piece of work for assessment.

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