Manuskript might be a bit more popular than UXpin. We know about 1 link to it since March 2021 and only 1 link to UXpin. 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.
1st design a responsive website from templates that follow established design: UXPin.com . Most of the other prototyping solutions kinda felt like they're built for folks who can draw, sketch, or maybe organize their room and choose matching clothes. Not me. Not a designer, I can barely choose my own clothes, let alone design something. I can think in components though. I especially liked their storybook example.... Source: over 2 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: almost 3 years ago
Figma - Team-based interface design, Figma lets you collaborate on designs in real time.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Invision - Prototyping and collaboration for design teams
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.
Adobe XD - Adobe XD is an all-in-one UX/UI solution for designing websites, mobile apps and more.
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.