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I want to be able to customize my run commands, i.e. I want to be able to his ALT+F2, get the prompt screen and enter a phrase of my own choosing to run a certain program. I have researcher aliases and the ls command, but these don't seem to do it. Anyone know how I can do this?
The keyboard shortcut is going to depend on what Window Manager you are using (WindowMaker/Fluxbox/GNOME/KDE/IceWM). Most of them do allow you to bind keys to a specific command. So I would start with reading the documentation for the window manager you are using. Bind keys should be right in there.
From there, just setup an alias for the program that you want to run.
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