It's not necessarily a problem, but it's a smell. Modern object-oriented PHP development is done with autoloaders[1]: having to require_once every class file is unnecessary and brittle. It is odd that GAE doesn't provide its own autoloader for its provided classes, and I'd expect that to be addressed in the future.
???
this is not argument - spl_autoload very fast its allow only one call to load module - all developers use spl_autoload
APC its legacy and crappy as opcache. I think its smell from Zend. They stop (in old time) because their close ware Zend Studio must sell. And other get pain from that legacy. Im sorry.
All modules use require_once... well, well...
And other many issues...
But looks as massive code. Maybe translated automatic.