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When running a b3 file, a check should be made that the file is not dirty. If file is dirty, a dialog should be displayed asking if the user wants to save the file first. If the file is not saved, it should not be executed. The reason why this is important is that linking and validation takes place when the file is saved. An unsaved instance may have stale data. There are currently two execution handlers (one calls the other), so the functionality can be made in one place (although it may be different later when also running headless commands).
With the separation between model and evaluator that took place long time ago, this issue is not a blocker - it works just fine to run the dirty model state if that is what a user wants to do. User should still be prompted warned and given the option to save.