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Edit: There is now a new version of Programmer Dvorak that works with key combinations like ⌃A, so the instructions below are no longer needed. ◊ Option modifier is currently non-functional. Also, you cannot replace a default Roman layout with this one. Control keys should now be functional. Option worked everywhere I tested, so non-functional could ...

OK - I've just downloaded NetBeans and I see the same issue. I think that this may be a JAVA issue, as both the IDEs you mentioned are JAVA applications. Cocoa apps such as TextMate seem to work fine. It may not be the answer you want - but if you want to use the Dvorak layout and have modifier keys work correctly, use an IDE that's not written in ...