Removing products and categories from the database
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This should remove all the products and their related records.
- TRUNCATE TABLE `catalog_product_entity`;
Removing categories requires bit more actions.
- TRUNCATE TABLE `catalog_category_entity`;
- DELETE FROM `catalog_category_tree` WHERE `entity_id`<>1;
After that you will have to create root categories for your stores and assign them to stores in configuration:
admin menu / system / configuration / catalog - choose a store, choose Root Category.