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Which file of wordpress manage the plugins functionalities. For example if a have to insert another rule in a plugin functionality where i go to modify?

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Modifying core WP files is considered extremely bad practice and almost never required to accomplish things. Please add some details on what exactly you want done so you get good answers. – Rarst Sep 8 '11 at 21:43
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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.

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