Thanks to you both.
I managed to add a menu item to the tools menu (though in the second section along with "More tools" rather than in the main menu with Calibre, Wallabag, etc, but still).
But I still have a lot to figure out with how settings are managed.
My plugin uses a configuration.lua file for the main user configurable stuff. So I'm looking at how koreader handles settings (I guess G_reader_settings?) and how to make my settings work the right way.
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