Some people say that unthemed Gnome looks a little unsightly, and they might be right. However, luckily all applications made using PHP-GTK happily work with GTK+ 1.x themes with no additional work. I myself have Gnome 2.6 installed, and so I needed to specifically install a GTK1 theme as GTK2 themes do not work with PHP-GTK or other GTK1 apps.
Anyhow, themes are all transparent to your scripts - you cannot tell whether a particular theme is enabled or not, and neither should you need to as your scripts will adapt to what the user selects.
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