
Manuskript
Scrivener
bibisco
yWriter
oStorybook
Novelize
BlankPage
Novlr
PullMark
Obsidian.md
Joplin
Logseq
Zettlr
Typora
SiYuan
Clearly Markdown
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.
Obsidian.md - A second brain, for you, forever. Obsidian is a powerful knowledge base that works on top of a local folder of plain text Markdown files.
bibisco - bibisco is a novel writing software.
Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.
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.
Logseq - Logseq is a local-first, non-linear, outliner notebook for organizing and sharing your personal knowledge base.