
Manuskript
Scrivener
bibisco
yWriter
oStorybook
Novelize
BlankPage
Novlr
thiscodeWorks
CodeKeep
CodeMyUI
30 seconds of code
Codespace
Forge
Creative Tim Bits
Anyfiddle
Manuskript
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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 5 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
CodeKeep - Codekeep lets you store and share bits of code and text with other users. Snippets can be organized into folders/labels for instant reuse.
bibisco - bibisco is a novel writing software.
CodeMyUI - Handpicked code snippets you can use in your web projects
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.
30 seconds of code - JS snippets that you can understand in 30 seconds or less.