Based on our record, FreeMind should be more popular than Manuskript. It has been mentiond 3 times 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.
Freemind and Freeplane are two mind mapping applications that have been around for years. Source: over 1 year ago
Download: https://sourceforge.net/projects/freemind/. Source: almost 3 years ago
Some others you might be interested in are yEd, or Freemind or other mind-mapping software. Possibly see whether BPMN is relevant. Source: about 3 years ago
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
Xmind - Xmind is a brainstorming and mind mapping application.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
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.
TheBrain - TheBrain: The Ultimate Digital Memory
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.