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I always found the Run command tool very difficult to understand at first, and then it made sense. Til I need to set it up from scratch again down the road and figure it out again.
But you can do great things with it, especially as far as creating folders, moving or deleting files, etc.
I made a macro tool to delete the automatically created .BAK files that Alteryx creates, particularly useful when your output is multiple worksheets into an Excel file - your report folder will have a .BAK file for each Excel file that gets created. Plop the macro into your workflow and it'll delete any .BAKs each time it runs