Manuskript
Scrivener
yWriter
StoryMill
bibisco
Novelize
BlankPage
oStorybook
Chronica
Fantasia Archive
World Scribe
Obsidian.md
Campfire Pro
ChronoGrapher
TiddlyWiki
Joplin
Manuskript ChronicaBased 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
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Fantasia Archive - Free offline worldbuilding and story creation tool with dozens of templates, complex tagging options, document linking, and project-wide search. Template examples: characters, places, events, religions, currencies, magic, species, languages.
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.
World Scribe - World Scribe is a platform that eases the creation process if novel and allows users to keep track of important elements in their world.
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.
Obsidian.md - A second brain, for you, forever. Obsidian is a powerful knowledge base that works on top of a local folder of plain text Markdown files.