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: almost 3 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Turnitin - Turnitin is preferred by educational institutions around the world for preventing plagiarism. Instructors at all levels of education can request that students use the service to submit papers, and Turnitin checks those papers for plagiarism.
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.
Unicheck - The plagiarism checker Unplag scans across the internet, repositories, open sources content and databases. It delivers real-time results and has no cached data.
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.
ProWritingAid - For the smarter writer. A grammar checker, style editor, and writing mentor in one package.