Manuskript
Scrivener
yWriter
StoryMill
bibisco
oStorybook
Novelize
Novlr
Freeplane
Xmind
FreeMind
vym
SuperNotecard
Visual Understanding Environment
MindMeister
Linked Ideas
Manuskript FreeplaneFreeplane began as a fork of the Freemind project. While maintaining comparability with Freemind file format, it has far outpaced in features and development. As of 3/5/2022, the latest Freeplane update (1.9.3) is 3/5/2022 vs Freemind was last updated (1.0.1) 2/5/2016. Active, helpful community.
Based 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.
Xmind - Xmind is a brainstorming and mind mapping application.
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.
FreeMind - FreeMind is a premier free mind-mapping software written in Java.
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.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.