Manuskript
Scrivener
yWriter
StoryMill
bibisco
Novelize
BlankPage
oStorybook
GitKraken Glo Boards
GitHub for Atom
KanbanFlow
Hygger
Trello
Kitemaker
Flow-e
Triage & Timeline by Linear
Manuskript GitKraken Glo BoardsBased 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: almost 3 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
GitHub for Atom - Git and GitHub integration right inside Atom
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.
KanbanFlow - KanbanFlow is a Lean project management tool allowing real-time collaboration between team members. Supports the Pomodoro technique for time tracking.
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.
Hygger - Hygger - is an Agile project management tool with built-in prioritization.