Before this disappears from my IRC scroll back...

<Glara> Instead of each core module having it's own variable, couldn't they be packed into a single array?
<Glara> So we'd do $bot -> core['whois'] instead of $bot -> whois = &$whoiscache;
<Glara> $this -> bot -> core['whois'] -> lookup($name);
<Glara> anyone could create a "core" module to share functions without editing Bot.php...
<Glara> Just thinking out loud.
01:28PM <Khalem> A valid suggestion
01:29PM <Naturalistic> Aye
01:29PM <Khalem> Slightly more typing, a slight inconvenience for a gain
<Glara> Bigger inconvenience to edit Bot.php for any custom core modules
<Glara> Upgrading to a new bugfix release replaces anything custom in Bot.php.
01:32PM <Naturalistic> yes, like Vhab's bot... you can't edit the core :p
<Glara> useful stuff has come out of core customizations though
<Glara> but there seem to be workarounds to do the same thing without changing the actual core files.
01:39PM <Khalem> Actually, it could be made more robust by using a function to  do the actual registering
01:39PM <Khalem> But again, if a developer screws up the bot core with his core hooks, it's fairly obvious
<Glara> Khalem: that would probably be a good idea to keep people from clobbering another module.
<Glara> and keeping registered module names unique.

So I went ahead and fiddled a bit and came up with a simple api registration function. By default it won't reset an existing function, but you can pass TRUE as the third function parameter if you're really really sure you want to clobber any existing class reference, though there is no protection from someone else doing the same to you in their module. I added log functions so that if something funky goes on, logs can be reviewed to see registrations.

Add to Bot.php around line 71:
    var $api;

Add to Bot.php around line 805:
    /*
    Registers APIs
    */
    function register_api($apiname, &$apiref, $replace=FALSE)
    { // Start function register_api()
        if (isset($this -> api[$apiname]))
        {
            if ($override) // Register the api, replace existing registration.
            {
                $this -> api[$apiname] = $apiref;
                $this -> log("API", "REG", "Reregistered API ".$apiname);
                return TRUE;
            }
            else // Don't register the api over the existing registered api.
            {
                $this -> log("API", "REG", "Did not register API ".$apiname." because it is already registered.");
                return FALSE;
            }
        }
        else // API is not set, so register it.
        {
            $this -> api[$apiname] = $apiref;
            $this -> log("API", "REG", "Register new API ".$apiname);
            return TRUE;
        }
    } // End function register_api()

Test modules attached. APITest1.php registers itself, APITest2.php uses APITest1 functions.

Like Nesi said, it's not needed to edit the Bot.php just to add another Core class. All you need to do is $bot -> myclass = &$myclass; in the myclass.php. Then you can call $this -> bot -> myclass everywhere.

Still a default way to add new core modules can never harm, especially with your collision check. You just got to rename the variable $overwrite to $replace in your api function (or the other way around). Right now that check can never be true