Is there any plugin that reads the Bukkit permissions.yml and 'pretends' to be the Permissions plugin for other plugins that support that and not the new built-in permissions system? If not, is it possible that one can be made? It is annoying having to manage two different permissions systems at once.
Even better than that - there's a plugin which manages groups based on easy to configure groups in its own yml files - overriding permissions.yml and allowing you to have full groups functionality. On top of this - it also pretends to be the permissions plugin - allowing you to keep compatability with old, out of date plugins. Check out bPermissions.
Never mind, I'm an idiot - I didn't realize that SpaceManic's "PermissionsBukkit" and "SuperpermsBridge" were two different things, and that together they do exactly what I want.