Which file of wordpress manage plugins functionalities?

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There should never be a case where you edit the core. Filters and actions were created so plugin developers could navigate the intricacies of WordPress wihtout touching core files. You should reference the following:

There are quite a few undocumented filters that I find when viewing WP core. If you do go to core, I would look for a filter that’s being used in the area you wish to alter WordPress rather than change the file outright.