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I'm a big fan of OneNote, which is designed as a digital notebook with separate pages, tabs and even tab groupings in each notebook. There's an official onenote app and mobilenoter, both of which could sync with desktop onenote if you like.
OneNote's structure is flexible and really fits the way I think, to the point that I not only keep notes external to the story there, I also write there. I can keep everything story related in one quickly reference-able section with the story itself, and quickly move between stories. I only export to a word processor when I'm ready to format it. But one could use it less comprehensively as well.
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