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I installed Docky in Ubuntu and I have it set to autohide. One problem is that if a window is maximized, then the docky is blocked. In order to see it, I have to unmaximize or moved windows. Can docky be made to appear above other windows?

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You can use devilspie to handle several behaviours under your Gnome's window manager, for instance the "always on top" you are searching for. Here's an example.

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