Scenes should be part of chapters.
The structure of a book is logically broken down by chapters, and then scenes within a chapter. But when I add a scene, it goes into "Notes". Each Scene should be able to be included in a Chapter, and reorganized as necessary, IMO (moved to other chapters, reorganized, etc).

We changed this behavior in Shaxpir 3.0, released on October 26, 2016. Under the new system, scenes are now nested within chapters, exactly as suggested in this post.
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Chris commented
Quoll does the same thing, drives me crazy and away so I'm looking for another writing vehicle...
When all the download programs like Scrivener, Writeitnow, writeway, Ywriter5 and more do it with scenes within the Chapters and thats where you write your pose it just doesn't make since to try an reinvent it.. -
Ernesto A. Ospina commented
This also confused me at first. Like Jamie DeBree, my writing process definitely requires scenes within chapters and my initial attempt to use "scenes" that way was frustrating. Now that I understand the intent behind this feature, I think it is certainly helpful, and the concern being expressed on this chain can be addressed by calling these "Scene Ideas" or something to make clear this isn't where one's draft scenes should go, rather support material for the chapters and sub-chapter scenes.
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M Harold Page commented
Ah. But a chapter **break*** can be a structural element.
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Jamie DeBree commented
Thanks for clarifying, Benji....I didn't realize (or remember from the video) that chapters could be arranged into levels. I created a few different "low level" chapters and named them "Scene 1" and "Scene 2" under Chapter 1, and that would work (as long as it will all flow together with the option to remove chapter headings/names once the export function is in place).
Scene notes make sense to me too...as I always write a brief synopsis about each scene. So I can connect a "Note Scene" to a "Chapter Scene" and that would work as far as organizing things goes. I'll try that.
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AdminBenji Smith (Founder, Shaxpir) commented
The intention with this feature was for a "Scene" content to contain notes about your scene, while the actual prose content of the scene would be written within a "Chapter". Perhaps that isn't clear enough...
Chapters can be arranged hierarchically, so you can treat the lowest-level chapters as scenes, from a prose-writing perspective.
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Lon commented
Agreed.
Also, the title, "Notes" to me, is really not the place to have a scene anyway. My apologies to Bengi, but in my work-world, a "NOTES" are the things I need to take care of....background info to keep in mind while I'm writing...corrections or research I still need to do. It can be a lot of things, but it is not "SCENES", IMO.
Also, once I have a dozen or so chapters, and I add a Scene, I see how a connection is added to a chapter. However, the scene can't be physicallyl moved to nest under the assigned chapter. In a production environment, I might have to look at every scene and every connection to make sure I'm working on the correct part of my work.
Selecting a chapter, and THEN, adding a SCENE, which would nest under that chapter, makes the most sense to me...along with the ability to rearrange those scenes as necessary, if I want to re-order my writing, for some reason.