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Have a look to the article here http://developers.facebook.com/blog/.
Is it going to change things on the way the module works ?
This will cause a problem because in Drupal we need to parse the request parameter before modules are loaded. This is done in fb_settings.inc, you can see the code there.
Unfortunately we will now need the secret to parse the parameters, but we don't know the secret until after the fb_app.module is loaded. In order to know the secret before then, it will have to be set in your settings.php. In other words you'll have to copy and paste the application apikey and secret into settings.php instead of a form at admin >> site building >> facebook apps.
Or perhaps the fb_app module will need to write the settings to a php file instead of saving to database. I'm not really sure.