So it is set by Menu->View->Change Colour Scheme..., which you can change while Geany is running, but not from the command line.

Well, you can't readily, but it's easy enough to either use a separate configuration directory (Geany's -c switch) or write a short sed command to alter the configuration before starting.

…Or possibly write a small plugin that would change the color scheme depending on the time, or some other global setting.

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