Manuskript
Scrivener
yWriter
StoryMill
bibisco
Novelize
BlankPage
oStorybook
Tech Doc Assistant
Boomerang Respondable
Just Not Sorry
Mailbutler
TheRightMargin
Analyze My Writing
Writefull
EngageBay
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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.
Boomerang Respondable - Write perfect emails with Artificial Intelligence
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.
Just Not Sorry - Highlight 'weak' words so you can edit them out
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.
Mailbutler - Mailbutler adds lacking functionality to email clients and increases your productivity