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You should never work on core files which are inside wp-admin and wp-includes folder.

You’ll be just working on wp-content folder.

If you’re developing a plugin, you can directly put the code in your main plugin file or you can put the file inside of your plugin folder and include that file in the plugins main file.

Or if you’re working with a theme, you can put the code directly in functions.php or create the php file inside your theme folder and include that file in functions.php