Michael,
After some research, I think the deprecation warning comes from the PHP version I am using (5.3.10) rather than from WordPress.
I edited line 65 of main.php and removed the pass-by-reference ampersand, and the warning disappeared. The change should not affect the behavior of the code (cfr https://us1.php.net/call_user_func_array).
Changed:
return call_user_func_array($method,&$args);
to
return call_user_func_array($method,$args);