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Caffeine for Linux 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: almost 3 years ago
If you wanted to do something fancy.. Something like this: https://launchpad.net/caffeine. Source: almost 2 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Caffeine for Windows - Prevent your computer from going to sleep
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.
Caffeine for Mac - Caffeine is a tiny program that puts an icon in the right side of your menu bar.
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.
KeepingYouAwake - A Caffeine clone for macOS Yosemite, El Capitan and Sierra (including Dark Mode).