I managed to solve this by creating a new "external tool" run config that executes a blank batch file. In the run config, you can have it refresh the workspace when complete. Then I created a macro using Practically Macro that 1) executes the last external tool run config (refreshing the workspace), then 2) executes the last debug run config (running my app). If you uncheck "Allocate console" then the completed external tool entry won't show up in the debug window.
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