Step 1: Set your preferences

- Create a notepad file and name it "permissions".

The syntax is:

groups:
group name:
prefix: '&0(&#PREFIX&#)&7'
permissions:
- node
- node
- ...
options:
rank: '#'
Prefix: The prefix is an optional. To set a prefix, you must use the following structure

'&0(&#PREFIX&#)&7 '

You can replace the # with different numbers, to set different colors. Here's a list for the MC servers colors.

An example:

prefix '&0(&8Member&0)&7 '

Note: The prefix won't show up unless you enable the chatmanager (Included in PEX) or install another chat manager plugin.

Permissions: You can add the permissions node here. (I'll explain in detail what the nodes are and how to set them)

Options:
Rank: Usually, "1" is the admin (If your rank is "1", you can't be promoted: the "1" is the
max. rank you can get.)

Rank example:
-Guests (default group): '400'
-Members: '300'
-Moderators: '200'
-Admins: '100'
-Owners: '1'

The Nodes:

The nodes are NOT that complicated, do not panic!

They are the REAL "permissions settings"; with the nodes you can allow/negate a server command (Or an installed plugin command).

This is the nodes syntax:

permissions:
- node

Notes:
The nodes' structure is: DASH (This little mark - ), SPACE, NODE ( - node );
To negate a node, the structure is the same, but you must put a DASH before the node ( - -node ).
The asterisk ( * ) allows every command of the node selected (modifyworld.* allows every command of the general node modifyworld)

An example:

I need to add the node modifyworld.* (which allows the player to interact with the world) to the group"Member",

and I need to remove the ability of placing TNT (TNT's ID: 46), with the node modifyworld.blocks.place.<blockID>

This is the syntax:

Member:
prefix: '&0(&#PREFIX&#)&7 '
permissions:
- -modifyworld.blocks.place.46
- modifyworld.*
options:
rank: '#'

modifyworld.* allows the player to use EVERY command of the modifyworld nodes (placing TNT too),
so you must put -modifyworld.blocks.place.46 before the node modifyworld.*.

Nodes lists:
Bukkit nodes: The basic nodes are the bukkit ones. You can find them here.
Modifyworld nodes: They regulate the player(s) interaction with the world(s). You can find them here.

Step 2: Saving the file.

Finally save the file as .YML (File>Save as; rename the file "permissions.yml" and select the option
"All files" in the drop-down menu)
Now your permissions plugin should be ready!

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Thanks for using my Guide for how to set up Permissions on your Bukkkit Minecraft Server!

Look on my Profile for how to use GroupManager!
Links:

PermissionsEX Basic setup (Basic guide)
PermissionsEX Advanced setup (Advanced guide)
Bukkit.org (Bukkit)