Bug 892397 - Specify hidden apps in their respective manifests

Fix for [#892397](https://bugzilla.mozilla.org/show_bug.cgi?id=892397). This moves the responsibility of hiding apps to the manifest files of the apps themselves.

We're adding a field to the manifest so that might be an undesired change. The code in settings/ that is removed is no longer necessary. If an application is not certified, it'll always show up in the settings, if it's certified, only when it has permissions that can be set.