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What exactly does Compiz-Fusion do and why am I better for not using it? The wiki didn't tell me much.
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Compiz does all of those little desktop effects you may have seen on the web. Like the desktop that looks like a cube rotating around, or how windows wiggle a bit when you drag them across the screen, or how things look like they are being sucked into the panel when you minimize them. To be honest it is a bunch of graphical fluff that creates an overhead that a lot of things do not play well with.
Flash is one of those things that does not play well with Compiz. There is a way to fix it by modifying you /etc/X11/xorg.conf, but I have yet to see a straight forward how to guide on it. Personally I disable it on my PC even though I have a video card and a system that could easily support it.