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"Debug Configurations..." and "Run Configurations..." only differ in a single button (Run/Debug)? Please consider merging both dialogs into a single one with two buttons: "Debug" and "Run". Scenario: I create a new Run Configuration and enter various settings at which point I realize that I don't want Run but Debug mode. I now have to close Run Configurations and open Debug Configurations just to click Debug.
There are other aspects like Remote Debugging is not available for Run. And it's extendible like if you have Yourkit installed, you can have more Configuration available. This concept is extendible and different properties can be changed for each configuration.
The tragedy of the egg-laying-wool-milk-pig: At some point, even simple things are terribly complex. If merging the dialogs is a no-go for various reasons, why not just show both buttons on both dialogs (or associate a key modify to invert "Run" to "Debug and vice-versa)?