
Manuskript
Scrivener
yWriter
oStorybook
Novelize
bibisco
BlankPage
Novlr
GNU Make
CMake
SCons
SBT
npm
Gradle
Brunch
Ninja Build
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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.
CMake - CMake is an open-source, cross-platform family of tools designed to build, test and package software.
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.
SCons - SCons is an Open Source software construction toolโthat is, a next-generation build tool.
oStorybook - oStorybook : a free Open Source novel writing program for creative writers
SBT - SBT is a build tool for Scala, like Ant or Maven but with hieroglyphics.