I have written about Twine before in 2009 and 2013. It has been actively developed and is now at version 2.0.10. Version 2 brings big changes. "The biggest change with the Twine editor is that it's now web-based. This means that it's usable on Linux computers out-of-the-box (it used to require manually installing some extra software dependencies) as well as tablets. Instead of opening files saved to your computer, wine stores your work in your web browser ..." "Because of this, if you use multiple web browsers or profiles on your computer, the stories saved to one browser will not be available to any other." Furthermore, "deleting your browser's history will also delete your stories." You can, however, archive your stories to the computer.
Twine 1.4.2 is still available for Windows and OS X.
Full disclosure: I don't write stories. I have never really used Twine for Note-Taking, though I think you could use it. One of the examples used on the Website is Melville's Moby Dick. There is absolutely no reason why you could not create a hypertext of other relatively short texts, like Immanuel Kant's Groundwork, for instance. I, myself, would prefer another application, of course