Encapsulate snap update permission operations in `PermissionController`

The [`SnapController.updateSnap()`](https://github.com/MetaMask/snaps-skunkworks/blob/5c1c0c92046bd6b016c518db773b5bb339a65861/packages/controllers/src/snaps/SnapController.ts#L1296) method performs some permission calculations that should occur in the `PermissionController`. In particular, it compares the permissions of an existing snap with that of a new version, revokes ones that no longer exist, and grants ones that were added. It accomplishes this by calling `PermissionController` actions. Ideally, these operations would be encapsulated within the `PermissionController`, while the approval request is managed by the `SnapController`.