Where to copy woocommerce files to in my custom theme to avoid editing the core plugin?

To override WooCommerce (WC) templates, put your modified templates in
custom_theme/woocommerce/template-category/template-name.php

Example: To override the admin order notification, copy:

wp-content/plugins/woocommerce/templates/emails/admin-new-order.php

to

wp-content/themes/yourtheme/woocommerce/emails/admin-new-order.php

WC Documentation Reference

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