I currently use a WP pludin, let's name it "PopUp_WP". I downloaded its opensource code. Then edited/customized lightly that code. Next, I want to disable "PopUp_WP" and add "PopUp_WP-edited" to my Wordpress, without deleting the original one.

What should I edit so the 2 plugins are not conflicting ? (not considered as the same entity)

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If you have deactivated the first one you should be able to use the new one without any hassle. When the plugin deactivated, WP core don't call any of it function or doesn't use any thing else from it. But if you activated both of them then it can cause function re-declaration etc.

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