If Eclipse (or another program) supports reassigning keyboard shortcuts, you can simply reassign the shortcut to the same physical key that QWERTY originally had when your keyboard is in Dvorak, so it looks like the same shortcut, but actually mapped to another key.
Otherwise, I just spend time studying the shortcuts in Dvorak. There may be pain at first, but you will be one more step towards being independent of QWERTY.
Tim
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