You can delete a category from a Custom Catalog. You can only delete categories that
are at the root of your Custom Catalog. You may need to remove associations from other
categories in order to move the category you want to delete to the root of the Custom
Catalog.
After opening Merchandising Manager via Launchpad on the login
screen:
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Click the Custom Catalogs tab, and then click the
Categories tab.
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Select the category that contains the subcategory you want to delete.
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From the toolbar, select Delete.
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Confirm the category deletion when prompted.
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Rebuild the custom catalog to apply the changes.