Configure which plugin custom post types get registered

Instead of having the users turn on and off the custom post types via a filter or action, you could have them select custom post types on an options page in the admin. When you have these selections in the database, your plugin can look at them at any point you need.

If you still want to use hooks in functions.php, you could set up a hook that would set the option in the database, instead of creating a new options page.

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