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I've found the brain to be the best software tool for this.
Sometimes you need supplementary software. Or hardware (like pen and paper).
Thanks for those, Pennlady, yWriter in particular looks useful for me. Scrivener looks like it does too much, and is less focused on fiction.
I've used Final Draft which has tools for structuring screenplays, including index cards" for scenes. I guess I'm looking for something like that, but which isn't focused on screenplays, but novels.