Manuskript
Scrivener
yWriter
StoryMill
bibisco
oStorybook
Novelize
Novlr
Pages
Google Docs
Adobe Acrobat DC
Wondershare PDFelement
Microsoft Word
Foxit PhantomPDF
Dropbox Paper
Conga Document Generation
ManuskriptBased 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
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Google Docs - Create a new document and edit with others at the same time -- from your computer, phone or tablet. Get stuff done with or without an internet connection. Use Docs to edit Word files. Free from Google.
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.
Adobe Acrobat DC - Make your job easier with Adobe Acrobat DC, the trusted PDF creator. Use Acrobat to convert, edit and sign PDF files at your desk or on the go.
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.
Wondershare PDFelement - All-in-one PDF editor