Geany uses a normal GTK toolbar and sets the primary-toolbar class on it, as expected for main toolbars. The theme is then responsible for styling it as it sees fit.

I'm not very surprised a theme would style the toolbar (and menubar) dark, as many themes do it. I don't think this is a bug in Geany; but please make sure Geany is the only GTK3 application with a toolbar that is styled this way: if it's the case, we might need to further track this down.

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