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You can delete a project by right-clicking its folder in the SQL Project Explorer and selecting
Delete.

When you delete a project, SQL Query Tuner will prompt you with a Confirm Project Delete dialog that asks you to confirm the deletion of the project, and offers you the option of deleting the project from the SQL Query Tuner interface, or deleting the project from the system. •

  • If you select Do not delete contents, the files and directory structure will be removed from SQL Project Explorer, but they will still exist on your machine.

...

  • If you select Also delete contents …, the files and directory structure will be removed from SQL Project Explorer and deleted from your machine.