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You're setting the launch configuration in the File Properties, and there is only one set of file properties per file. To run the same file with different configurations, create named entry points instead. These pair a selected file with a selected launch configuration. This can either be done from the OS Commands tool by selected Named Entry Point type of command or from the Named Entry Points dialog accessed from the Debug menu. A named entry point can be either executed (via OS Commands) or debugged (from the Debug menu).