Writing Outliner
Dynalist
Workflowy
OmniOutliner
Scrivener
ATnotes
iA Writer
Legend
Manuskript
Scrivener
yWriter
StoryMill
bibisco
oStorybook
Novelize
Novlr
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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: over 2 years ago
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Workflowy - A better way to organize your mind.
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.
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.
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.