client VS zim-desktop-wiki

Interesting take! It does seem to address a typical "intermediate" workflow; even though we prefer linear finished products, we often work by completing a hierarchy first. I've been using Gingko [1] for years, I find it eases the struggle of organizing the structure of a problem by both allowing endless expansion of levels, and easily collapsing it into a linear structure.

In your case, do you hold N contexts (N being the number of leaves in the tree)? Are the chats disconnected from each other? How do you propose to transition from an endless/unstructured canvas to some sort of a finished, organized deliverable?

1: https://gingkowriter.com/

In re-reading your post, it occurred to me that you might also want to look at parallel/ horizontal outliners like gingko https://gingkowriter.com/ or https://gingkoapp.com/ (there was talk of a desktop app) https://wavemaker.co.uk/blog/wavemaker-version-3-is-live Evergreennotes https://evergreennotes.com/ (I believe it is inspired by https://andymatuschak.org/ technique). speare.com and https://transno.com/ and https://innos.io are similar in look and feel (same development team I believe)

I haven't used this on a document as large as the final PhD manuscript, but I feel like it might be helpful to you: https://gingkowriter.com/

I'll slightly modify your argument; because Pure HTML does suck:

Why don't people make static sites with a simple "Markdown-or-Similar to HTML" converter, CSS, and vanilla JS...etc?

(This is what I do, btw -- http://zim-wiki.org + a template)

You should add Zim [1] to the "Personal Knowledge Management" section :)

[1] https://zim-wiki.org

https://meyerweb.com/eric/tools/s5/

And I just tweaked the CSS and added a bit of logic to included the possibility of one image per slide; as well as editing slides not with raw HTML but with https://zim-wiki.org (because that's what I'm really used to, I'm sure any Markdown thing would work just as well).

Absolutely; recently I realize I wish I'd never learned vim. I use too many other programs that are at least CUA-ish ( http://zim-wiki.org is the most important app I use ) and now I kind of want out. I haven't yet tried Modeless Vim, but that looks like my next experiment.

https://github.com/SebastianMuskalla/ModelessVim

It is so hard not to feel REALLY SMUG reading stuff like this, as someone who has run my own website as the working primary source for my college instruction for the past 15 years or so using https://zim-wiki.org. (before Markdown was much of a thing!)

It's borderline bizarre to have watched this method of doing things kind of die out, and then also come back in the form of "static site generators" -- which, frankly, are still way clunkier than this.

Write in Zim, export to html, rsync to site. Easy.