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Microsoft Visual Studio might be a bit more popular than Manuskript. We know about 1 link to it since March 2021 and only 1 link to Manuskript. 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
While the editor seems to old fashioned there isn't anything particularly wrong in using it for learning. Alternatively you can propose to your teacher about https://visualstudio.microsoft.com/vs/express/ . IMO editor is not a big factor when we are talking about high school learning. Source: about 3 years ago
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
IntelliJ IDEA - Capable and Ergonomic IDE for JVM
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.
Xcode - Xcode is Apple’s powerful integrated development environment for creating great apps for Mac, iPhone, and iPad. Xcode 4 includes the Xcode IDE, instruments, iOS Simulator, and the latest Mac OS X and iOS SDKs.
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.
Visual Studio Code - Build and debug modern web and cloud applications, by Microsoft