'xed' has its' own configurationsI was able to edit the XML for that to get it to do what I wanted.
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For me on Linux Mint Cinnamon both GTK2 Geany and GTK3 Geany and Xed follow the selected desktop theme. A majority of developers seem to think this is the "right thing" to do.

If you don't want an application to follow the theme you can have your own settings for the application in your personal GTK settings.

For GTK2 Geany the widget colours can be customised for specific apps using the selectors that are noted in the Geany manual in ~/.config/gtk2.0/.gtkrc.

For GTK3 Geany colours can be customised for specific applications using the CSS based syntax in ~/.config/gtk3.0/gtk.css

There is lots of guidance on how to use the GTK theming available on the web.

But desktop themes don't have settings for programming language syntactic elements, thats why Geany has its own filetype specific theming just for the editing window.

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