File A includes files B and C.
C thus has access to all the stuff defined in A and B, but C doesn't know that. How can I tell C that it actually has access so that IntelliSense works?
Perhaps a more clear example:
If master.php includes library.php and page.php then page.php has access to library.php, but there's no way for page.php to know that. I want to manually tell page.php that library.php is already included, and have Komodo save this in some meta data or project file.
The basic answer is that, depending on your Komodo settings, it will automatically gather it (though in my experience it's not 100% reliable). You can set which directories to automatically import for intellisense in the IDE settings. Two places I would check:
Go to Edit->Preferences->Code Intelligence in Komodo IDE and make sure 'Include all files and directories from the project base directory'
Go to Edit->Preferences->Languages->PHP and add any other directories to the import like Zend Framework, for instance.