I generally use PowerPoint for outlining my scenes (prose, not script). I put a general description of what the scene is on the slide, and then give more details in the notes section. I like that I can see all the scenes and the flow of the story in the slide sorter view. I can then easily move scenes around to better fit the pace or development of the story. However, this program has some drawbacks, especially when the number of scenes gets up above 25 or so. I end up doing separate PPts for different arcs. Is there any kind of writing software where you can view and shift scenes around like this?
You could try campfire, it's marketed as a worldbuilding and planning tool.
I've also looked at Scrivener, which may have a more familiar interface to that of PowerPoint.
WorldAnvil is another tool, although this one may or may not handle scene management as easily (I've not used this one extensively enough to figure that out yet), WorldAnvil will allow you to build a sort of Wiki for your novel and create links between characters, locations, events and all sorts of other details.
ARCHIVOS might be what you want. (Free account lets you build a world!) It allows you to create scenes, establish relationships between them. Characters (and relationships with them), plus a timeline. Lots of ways to link up info, but I don't know if it specifically links them to "scenes."
One feature I've asked for is multiple timelines in a single story setting -- so if I'm writing about the Adventures of Superman radio show, I can have an in-story timeline, and a broadcast-date timeline (for context).
So for you, 2-timelines may also allow you to have "storyline" timeline (what HAPPENS when) and "novel" timeline (when is the info presented). (I repeat, this doesn't seem to exist (yet) as a feature.)
This may work for you if scene-occurrence and scene-presentation match. Archivos is ALL about the relationships between and within people, events, locations.
First, ARCHIVOS helps Storytellers document the characters, places, and events of their stories, detailing the basic framework for the tale.
Then, Storytellers connect those story elements by defining the relationships between them that articulate not just the existence of the connection but also its nature (professional, personal, political, geographical, etc.).
The relationships in ARCHIVOS also support a hierarchy, like that of a parent to a child, or a manager to an employee. This framework will help identify and organize the structures within the story world.
As those structures become clear, Storytellers become true story architects, able to refine the and enhance the impact of their stories.
Here's info on how to create/arrange things: https://archivos.digital/getting-started-archivos/ (scroll to "adding story elements"
You can choose from the following list to define the Type of Story Element you’re creating:
Person* – from protagonists to the smallest walk-on role
Region* – worlds, continents, countries, counties, mountain ranges, forests, etc.
Location* – towns, buildings, landmarks, ruins, etc.
Organization – governments, guilds, religions, cabals, corporations, etc.
Item – relics, artifacts, unique tools, cars, ships, etc.
Event* – battles, treaties, plagues, births, deaths, graduations, etc.
Culture– ethnicity, as well as speculative cultures (elves, dwarves, giants, aliens, etc.)
Discipline – magic, kung-fu, cloak fighting, psionics, etc.
This link has information about the relationships you can see and manipulate: https://archivos.digital/story-web-archivos/
Disclosure - I became facebook friends with the guy who created this after I saw a demo at BaltiCon last year. When/if I have enough time/energy, I definitely want to play with it more. No actual connections to it, and I haven't used it in depth. Again - it's FREE to set up a single world and use all features!
I think Manuskript (http://www.theologeek.ch/manuskript/) might be what you want. It's a free and python based software so it runs on any system that can execute python.
I use it for all my projects. It's also in continuous development so if you have a specific feature in mind you would like you can suggest it and maybe the devs will add it.
I would check out Plottr, which is a newer program dedicated to plotting and planning out your stories. A lot of my friends prefer it to Scrivener for organizing scenes and ideas, etc. They have a free trial you can download, too.
If you just want to try something out then YWriter does exactly that and it is AFAIK the only novel writing software designed and developed by a working novelist, and best of it's completely 100% free, gratis and for nothing. You can download it from here: http://www.spacejock.com/yWriter6.html