Documentation Agency
Docusaurus
Devhints
GitBook
Archbee.io
Tettra
Stack Overflow Documentation
The Documentation Compendium
Manuskript
Scrivener
yWriter
StoryMill
bibisco
Novelize
BlankPage
oStorybook
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This is too biased for me IMHO. I do agree with some points, documentation IS amazing, and you are very likely under-documenting things. But documentation is not cheap to create, and specially it's not cheap to maintain. I've worked in multiple companies where the problem was too much documentation, and of course everyone was afraid to update or ghasps remove any piece of old documentation in case it... - Source: Hacker News / about 1 year 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
Docusaurus - Easy to maintain open source documentation websites
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Devhints - TL;DR for developer documentation
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.
GitBook - Modern Publishing, Simply taking your books from ideas to finished, polished books.
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.