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Do you mean transparency in a terminal emulator? Depends - the manual for your term would say - but it's usally 'aterm -tr' or the like. Not sure if that's what you mean, though. They're not so much clear as they take the root window image and use it as their own background.
Hm. Not sure - you mean in konqueror or nautilus? I can't remember but I think there's an option in the configuration menu to set backgrounds like that. I don't have those now but I seem to remember being able to do that. It'd be something like "Options>Wallpaper>Transparent", maybe. Hopefully someone who uses them will say for sure.
Yeah - that's mostly wallpaper. Konsole is a terminal emulator - it's either in settings or in a menu to the left with stuff about 'schemes' or some such. And the menu is transparent - that's alpha blend settings - probably in the 'kontrol panel' or whatever under 'themes' or 'styles' or something. I think it's a checkbox buried back there somewhere - or maybe I'm thinking of gnome.
Actually looks like a blend of wallpapers - part of it is the 'glass' wallpaper but I don't recognize the rest. And glass is blue, whereas that's given a greenish tint.
But anyway - just a transparent konsole and menu. Just a checkbox to check somewhere in the configuration areas.
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