In a new post to his blog Stanislav Malyshev talks about how Zend Studio users can get the tool to recognize new extensions by adding in stubs with PHPDocumentor markup.

If you have some extension, create stub file with PHPDOC descriptions [...] for each extension function, Studio will know to pick it up. You can put this file into Studio's prototypes directory - easiest way to find it is just write something like chdir() anywhere, select the name and press F3, the directory of the file that you'll get is the one you need.

Not wanting to have to generate all of the stubs himself, he created the Reflector script that will, when pointed at an extension, create the stub file with definitions for each method it can use. There's also the generator script that's a part of Zend Studio that works similarly.