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
Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.
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.
Google Keep - Capture notes, share them with others, and access them from your computer, phone or tablet. Free with a Google account.
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.