Cliff is spot on. The most your index.php script should know of your PMVC is the Facade and the only action it should initiate is the Facade's startup() method. You're on the right track with .htaccess. You could even go further and create "clean urls" that you can parse and pipe into your PMVC application for some pretty slick processing (data retrieval, AMF integration, templating, etc).
I've been thinking about doing some quick posts on different ways to instantiate a PMVC application in PHP but have been brutally swamped @ work. Stay tuned though, because the PHP community here is definitely going to continue to grow...
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