client VS catwiki

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've been using my CatWiki[1] for making notes since 2016 and find it quite easy to use. It stores notes as Markdown files on a local hard disk.

[1]: https://github.com/cabalamat/catwiki