Manuskript
Scrivener
yWriter
StoryMill
bibisco
Novelize
BlankPage
oStorybook
BlockRight
Blockai
Harvel
Patent Monk
Po.et
TMchecks
Atrium
Trademarkia
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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
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Blockai - Protect and claim ownership of your digital creations
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.
Harvel - Copyright protection tool scanning the web for illegal copies of your content, sending DMCA Takedowns to Google and hosting sites, in order to prevent revenue leak and increase sales.
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.
Patent Monk - The patent search engine you always wanted to exist