<p>The terminal configured in <code>Preferences->Tools->Terminal</code> is what application Geany opens as a subroces when you run build commands, by default. It would use whatever colour scheme mechanism it uses and is totally independent of Geany.</p>
<p>The builtin terminal in the Messages Window notebook at the bottom (or side in your case), is totally separate, it's a terminal widget builtin to Geany, and has nothing to do with xfce4-terminal or other terminals. The builtin terminal only lets you change the default background and foreground colours using <code>Preferences->Terminal</code>.</p>
<p>The colour scheme set for the editor widget where the code is, is again totally independent of any terminals, it's only used to style syntax highlighting of code in the documents notebook.</p>

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