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 Preferences->Terminal.

How can I determine where the terminal widget is getting it's colors from? $TERM from the terminal widget yields xterm, and yet the terminal widget does not respect any configuration of xterm, for example from .Xresources. It also doesn't get anything from whatever terminal you've configured. VTE3 doesn't have anything for configuring colors that I could find. The LS_COLORS environment variable still works at least ... but I'd really like to be able to set colors in a normal config file.

On another note, it's confusing that setting Preferences->Tools->Terminal doesn't affect the terminal widget in the message window. Intuitively you'd expect that setting the terminal set everything to do with the terminal (particularly the actual terminal that you see as a user). A tooltip or a more descriptive name would be good.

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