When "thumbing" modules, especially core modules, as far as I know it is a good idea to take the module specific tpl.php files, duplicate the ones you need, and modify them once they're in the relevant theme directory.

However, what if I want to modify a .inc file? Is it the same process as with tpl.php files, or is there a better workflow? Basically what I would like to do is change some of the user status messages found in user.admin.inc in the core Drupal 7 User module. I'm not sure if editing this file directly is a good idea. Thoughts?