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I ran into too much trouble trying to accommodate a structure with subdirectories, so I took the easy way out of creating a flat structure on import. I did this, knowing that it's trivial in Sigil to Restructure to Sigil Norm. It can even be included in a Toolchain after running the plugin. But really; any reading system or rendering engine that can't deal with a flat epub structure should be considered broken.
As for include_default_style_map=False, there is no current way, but I'll try to look into it.
I don't remember offhand how the split markers are generated, but I would assume that anything that CAN be mapped by Mammoth could be mapped to sigil's split marker. I've not altered Mammoth in that regard.
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