[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]
What was leftover by the end of my PhD submission process...
I used Trello for structuring my PhD argument and for tracking my progress during the drafting and redrafting of the final text.
Trello is primarily associated with the Kanban workflow / movement and as such it offers a fast and easy-on-the-eyes way to visualise structure, the passage of tasks through a particular workflow and so on.
It only works with an internet connection, however, which makes this a somewhat qualified recommendation. The mobile apps associated with Trello also lack an offline mode.
Tasks are split up into lists, and these are organised in a sequence. Thus for me, my lists at one point were my different chapters. It's easy to email things (links, notes to yourself, or anything else text-based) into your lists from outside Trello, so it can function as a useful 'bucket' where you can deposit things you want to research in the future, or just tasks that need to be performed for a certain chapter.
It's a way of seeing what needs to be done, or what you want to add to a particular chapter, at a single glance. Not essential, but I found it useful at certain junctions of the editing process.