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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: about 4 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Markdown to PDF - Super simple way to get your markdown files to PDF
oStorybook - oStorybook : a free Open Source novel writing program for creative writers
Publish Markdown - The simplest way to publish and share your Markdown
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.
Markdown by DaringFireball - Text-to-HTML conversion tool/syntax for web writers, by John Gruber