Ok, so the new bPermissions, it’s new, but don’t panic!
The file format is different, but an import feature will be added from the old bPermissions soon enough!
Commands are no longer customisable, but in return for this, I’ve significantly shortened them.
So commands, what’s new? Well... everything!
Firstly, they’ve been abstracted to a selection based system, this means that rather than specifying the thing you want to work on each time, you just select it and it remembers your selection.
/world home /user Notch /user addgroup admin /user addperm ^bukkit.command.stop /user meta prefix Mojang /permissions save
This code selects the world “home”, selects the user “Notch” from that world, then adds the admin group to him, and sets the “bukkit.command.stop” permission to false, stopping him from stopping your server! It then sets his prefix to “Mojang” and saves your changes.
(Changes are not saved to the file until you use the “/permissions save” command, changes are not applied to logged in players until you use the “/permissions reload” command)
Commands: (user/group have the same command arguments)
/world - displays your selected world /world NAME - selects a new world /user - displays your selected user /user NAME - selects a new user /user addgroup VALUE - adds a group to the user /user rmgroup VALUE - removes a group from the user /user setgroup VALUE - sets the users group to a specific one /user addperm VALUE - adds a permission to the user /user rmperm VALUE - removes a permission from the user /user list groups/perms - lists the users groups or permissions /user meta KEY VALUE - sets the metadata for that key to a specific value (used for chat prefix etc)
As for the files, Nijikokun had a shot at explaining the new files for me ;)
This is an example groups.yml
# This is ur joinin group, liek when they first join they get put in this basket default: default # these r liek baskets, each one has different purposes groups: # this basket would be something a god carries admin: # and deez are what that god could do permissions: - bPermissions.admin # and this is liek what other baskets they hold groups: - default # this is liek a peasant basket, low income people default: # they can touch and stuff, but not major changes permissions: - bPermissions.build - bPermissions.test # they can't carry any other baskets groups: 
users.yml follows the same format but does not have the "default: value" and has "users:" instead of "groups:"
There is a "default" users.yml and groups.yml in the root server directory, these are what files are copied from when they are created (if you add a new world for example)