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Well, for me personally, I get a lot out of org-noter. I like to write in org-mode but frequently find my editing skills are improved by exporting it to a more "readable" format. I then like to use the specific-note function to click on the exported pdf/whatever to add highly localized notes for myself, which are collected in a bidirectionally-linked org file for later review.
I wrote my own system called Org Novelist.
Thank you for your detailed answer - I am not OP but I just wanted to point out (in case you were unaware) that the great org-noter has recently found a new maintainer and the repo has moved here: https://github.com/org-noter/org-noter
I also use writeroom because I prefer its simplicity, but worth mentioning that olivetti is the more popular writing mode.
I use org-roam extensively for managing notes. Specifically, I more or less adhere to the principles or /r/zettlekasten when doing so, which is specifically geared towards taking notes for the purpose of writing (traditionally non-fiction). The rough idea is that notes are structured in a way such that you can browse them non-linearly: you can follow different paths through your notes, not just from the top of a document to the bottom, or from the 1st note to the last. And the act of looking through notes becomes a bit like having a conversation with your knowledge base.
I use something similar, called org-remark. By the description of both, they seem to share functionalities. Just mentioning it for visibility :)
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