MarkdownPad
Typora
Markdown by DaringFireball
StackEdit
Minimalist Markdown Editor
HedgeDoc
Rentry.co
Dillinger
Manuskript
Scrivener
yWriter
StoryMill
bibisco
oStorybook
Novelize
Novlr
MarkdownPad ManuskriptBased on our record, MarkdownPad should be more popular than Manuskript. It has been mentiond 2 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.
(Opened article in Reader mode in browser, copied it, pasted into Markdownpad, cleaned up article (removed image captions, MORE: lines), made the whole article a quote, and pasted here in the comments.). Source: almost 2 years ago
(I used http://markdownpad.com/ to quickly format the quoted article for posting here on Reddit). Source: about 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: over 2 years ago
Typora - A minimal Markdown reading & writing app.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Markdown by DaringFireball - Text-to-HTML conversion tool/syntax for web writers, by John Gruber
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.
StackEdit - Full-featured, open-source Markdown editor based on PageDown, the Markdown library used by Stack Overflow and the other Stack Exchange sites.
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.