"Dvorak - Qwerty ⌘" doesn't work for some applications

I recently switched to Dvorak, and I'm using the Dvorak - Qwerty ⌘ layout. It works in most situations, except some applications don't honor the Qwerty shortcuts. That is, if I were to press what would be command+c on a qwerty keyboard, some applications recognize it as command+j, which is the equivalent key in Dvorak. The applications I've noticed this in are Eclipse and Android Studio, both IDEs, and Terminal. I'm not sure how to deal with this problem. I would like to find a way to make my keyboard interpret all ⌘+{character} commands as Qwerty commands, but type in Dvorak otherwise. I'd prefer that the solution be extendable to things like ctrl+{character}, for Terminal shortcuts, and be extendable to other layouts, since I'm hoping to make the jump to Programmer Dvorak soon. Related: https://apple.stackexchange.com/questions/84350/some-dvorak-shortcuts-arent-working-10-8-2 (is about Dvorak, not Dvorak - Qwerty ⌘) https://apple.stackexchange.com/questions/13871/keyboard-shortcuts-with-dvorak-keymapping (does not address the issue of keybindings not working)