It's similar but simpler In the plugin folder there is a folder for each world containing a permissions.yml and a users.yml. The permissions yml handles the groups, nodes, prefixes, suffixes, and priorities. That's all! The users yml handles which player is in which group
RumbleIV There's a mirror.yml and in the config there is a global-permissions option. Thy doesn't really work so you have to look around a bit. The easiest way is to copy and paste in the permissions.yml from the preferred folder and paste in in all the others. EDIT: Dead-i it internally breaks some plugins. You may not notice it, but does break them.
PermissionsEx is still working perfectly fine for me on 1.6.2 And as far as them changing it, another person is taking over the development instead as far as i know.