Manuskript
Scrivener
yWriter
StoryMill
Novelize
bibisco
BlankPage
oStorybook
Monkkee
Ideanote
The Guide
Idea Notebook
x-whnb
Scrapbox
RunaBook
Reminisce Journal
Manuskript MonkkeeMonkkee is so secure that the entries can be read only by you. If you lost the password it is lost forever. No one has access to even your password. It provides client side encryption i.e the entries are encrypted even before they are transferred to the server. It is easy to use. You can categorize your diary entries using tags.
Based on our record, Manuskript seems to be more popular. It has been mentiond 1 time 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.
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
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Ideanote - Ideanote is the #1 rated Idea Management solution for companies of all sizes. Collect, develop and manage more of the right ideas from customers and employees to drive your growth.
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.
The Guide - The Guide is a two-pane outliner - a program that allows you to arrange text notes in a tree-like...
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.
Idea Notebook - Idea Notebook is an app that allows you to keep track of your logs business ideas and track as well as organize them.