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Based on our record, Manuskript seems to be more popular. It has been mentiond 1 time since March 2021. We are tracking product recommendations and mentions on various public social media platforms and blogs. They can help you identify which product is more popular and what people think of it.
Looks like you want something that integrates well with your workflow. The closest to your description seems to be Manuskript although I haven't used it. But your requirement of "keeping notes and frameworks and linking back and forth" should be possible by stitching together existing Linux tools using a syntax like markdown or asciidoc so that you can use any text editor to write your story and use external tools... Source: almost 3 years ago
TiddlyMap - An interactive concept- and mind-mapping plugin for the personal note-taking software TiddlyWiki based on the Vis.js library. It's free and open-source!
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Wisdomap - Wisdomap Medicine is a study aid that helps medical students create differential diagnoses and suitable management plans from a presenting complaint and structured revision notes.
yWriter - Free writing software designed by the author of the Hal Spacejock and Hal Junior series. yWriter6 helps you write a book by organising chapters, scenes, characters and locations in an easy-to-use interface.
IOctopus - IOctopus is an online mind map service for a dive deep into the mind for the best ideas.
StoryMill - Developers and publishers of Mac, Win, and iOS productivity, home and office and writing software such as MacGourmet, Paperless and many more. Based in MN.