Heimer
SuperNotecard
Freeplane
vym
Linked Ideas
Visual Understanding Environment
Pencil Project
OmniOutliner
Manuskript
Scrivener
yWriter
StoryMill
Novelize
BlankPage
bibisco
oStorybook
Heimer 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
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.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Freeplane - Freeplane is a powerful and free software for building mind maps.
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.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
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.