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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: over 2 years ago
NotePlan - Make plans inside an individual markdown note for every day in your calendar. Use it as a journal for your daily tasks and plan todos in advance. For Mac, iPhone and iPad.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Mochi - Write notes and flashcards with Markdown and study them with spaced repetition.
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.
Inkdrop - The note-taking app with robust Markdown editor, supporting macOS, Windows, and Linux.
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.