I’m considering writing a theological book. While part of a university 3 years back I used OneNote, Zotero and MS Word (integrated nicely with Zotero). I plan to draw on a wide range of academic and non-academic sources. I loved Zotero. I’m currently using Obsidian for most of my day to day.
It may never be published, but it should be fun to do. As such, I don’t have to use organisationally defined software.
Technology has moved on. What are people using these days?
For long-form writing involving research and lots of brainstorming, reorganization, annotations, etc., there is nothing better than Scrivener. Once you have your draft reasonably organized, you can choose to finish your work completely in Scrivener (maybe publishing an ebook, for example) or “compile” (export) it into many other formats such as Markdown, TeX, Word, etc., to finish your work in another tool.
Scrivener uses a “one-file-per-project” approach, in contrast to “all-your-writing-in-one-place” approach of the Ulysses.
Scrivener’s research tools and editing features are great. You can store many document formats in the research folder, annotate them, view them side-by-side as you write, etc.
Scrivener’s outlining and organizational tools are beyond comparison for writers.
For long-form academic writing, I use Scrivener as my preferred writing environment. I use Zotero for inserting citation keys. Then I export to Quarto as a Book project to process any Python or R code, figures, bibliography, etc., and to render the finished product. (Quarto uses Pandoc and Markdown, LaTeX, or Typst under the hood.)
I concur, Scrivener is where I’m writing a large 35+ chapter book.
I’ve looked at Scrivener a few times, but the biggest strike against it for me is that the only way to sync data between devices is to use Dropbox and I’m not comfortable using dropbox.
Of course you can use Scrivener only on one device if you wish.
I believe that it’s a technical restriction on the package style storage of information which doesn’t play nicely with icloud syncing, but it’s a massive restriction in this day and age, and I can’t believe that after this being a restriction for so long that it’s not been tackled.
I too dislike using Dropbox to sync Scrivener. This is why I only use Scrivener for one project – a book. It is excellent for that purpose. I use it in conjunction with Endnote for citations and bibliographies and DEVONthink for research articles.
I use Scrivener for a long time for bug writing projects. Two macs and two iOS devices. I have no issues or concerns with it or using Dropbox to sync through all devices.
I’m a keen Zotero user as well and I think you’d have no issue still using it.
Long form writing, I did all my thesis in LaTeX and I’d probably use it again for similar if I needed to (in fact, I will need to write a technical report for my chartership, so it’ll come out for that I imagine). However, it’s a lot of learning, especially if your layout needs will be simple. I never got in to Scrivener myself as when I discovered it, I was too far down the LaTeX rabbit hole!
Some of the markdown tools seem to be good for long form writing now but are fairly simple.
I’d say that unless you want to learn new tools, maybe it’s best sticking with what you know?
Maybe another question for OP is whether there was anything you felt was missing and/or added friction in your previous setup? There could be other tools available now to address old concerns.
Good question. Zotero worked very well (and has come on a long way since then) and Word worked fine (although I was never producing anything book length). The biggest challenge was perhaps with OneNote, which worked reasonably well but wasn’t great for reorganising and processing information.
I did use MindNode (or something similar) for a while which I think I would reproduce as it’s an incredibly effective way (for me) to organise and change a structure.
I can’t remember when OneNote updated, but it did at some point maybe 3-4 years ago and then it wasn’t the OneNote I knew and loved any more. It’s still a good app (or was when I last used it), but just be aware that depending on when you last looked at it it has changed.
How are you going to manage all your reference material? That would be my first question, and the answer for me is DevonThink. Writing comes after (or alongside!) research.
I’m not fussy about the writing bit, but I am fussy about the research bit. A lot of my text actually just starts in plain markdown docs, then I bring the fragments together in Google Docs or Pages or something else depending on what I’m up to. This mimics how I used to compile papers before I became a keen tech user - I tended to write bits in plain text files or by hand on paper (depending on where I was, this was prior to smart phones) then pull it together later.
I’d actually forgotten until I read this thread that I’ve bought Scrivener on Mac and iOS, I’ve just never used it!
Since you’re doing this project for fun, might I also suggest that you read Umberto Eco’s How to Write a Thesis first as it’s a good text on how to research and write. I read it as an adult and wished I’d read it as a student!
This has been helpful in helping me remember exactly what my process was (which worked for me). I used Zotero more or less exclusively as my reference material manager (although I didn’t use Markdown then). Most of my preliminary writing and pulling of quotes was in a very, very long Word document which I then distilled, extracted and reorganised content from.
I dare say that process could use some of the card based systems now available, something like Logseq, or perhaps even Obsidian canvas. It was certainly more time consuming than it needed to be back in the day.
Of course, on one level this is procrastination before actually researching and writing! 
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I’ve always set up a folder in iCloud, without any issues…
The developers don’t recommend using iCloud so I’ve tried away from it. They are working on an alternative app that does use iCloud.
Better to take 5 minutes to look at a map before the journey and save 5 hours later being lost! 
Have you considered using one of the new AI tools like NotebookLM?
I hadn’t, and will have a play. It does look like it could have incredible potential for distilling large amounts of information and triggering ideas.
My biggest concern is Google pulling their “experiment”, so I perhaps need to consider sustainability if it turns into a long term project.
I understand. The latest news I’ve seen is they have released it in 200+ countries.