OmniOutliner
Workflowy
Dynalist
SuperNotecard
Linked Ideas
Visual Understanding Environment
vym
Freeplane
Manuskript
Scrivener
yWriter
StoryMill
bibisco
oStorybook
Novelize
Novlr
OmniOutliner 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
Workflowy - A better way to organize your mind.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
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.
SuperNotecard - Introducing SuperNotecard. SuperNotecard is an online writing tool that features virtual notecards to help arrange facts or scenes, track details, organize paragraphs, and clarify your composition process.
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.