My Storybook might be a bit more popular than Manuskript. We know about 1 link to it since March 2021 and only 1 link to Manuskript. 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
I have OSDD but maybe this would work for you too. My grownup part wrote a book for me. It explains important things I need to know. They read it to me sometimes when I need to hear those things again. They made pictures to go with the words so I like it better and it makes more sense. They used mystorybook.com and it's easy but maybe if you're better at art you would do your own thing or use a more complex tool. Source: about 3 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Storyboard That - Storyboard That is the world's best online storyboard creator.
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.
Storybird - Visual storytelling community
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.
Storyboarder - Storyboarder makes it easy to visualize a story as fast you can draw stick figures.