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?
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.