Bukkit

What is the issue? I don't know what to do beyond this point and need some help to sort the file to be able to be properly used.

Please provide any additional information below.

I never understood why people do this:

- ^group.default
groups:
- default

It's redundant. You're saying "do everything this group does" when you stick it under groups, but then you take away all those permissions by negating it in the nodes.

admin:
permissions:
- 16d2f8ee-2047-4c4a-b610-edbe4914d1ac

Why is there a UUID as a permission here?

You also do this?
- citizens.npc.limit.97
- citizens.npc.limit.98
- citizens.npc.limit.99
etc etc;

You don't need repeating permission nodes like that from plugins. You're making your file a lot bigger than it needs to be, and probably confusing plugins to boot.

An example is this:
- core.* (Already give EVERY permission for the plugin possible)

You don't need ANY of these:
- core.board
- core.board.cycle
- core.board.list
- core.board.show
- core.board.stop
- core.board.toggle
- core.chat
- core.chat.list
- core.chat.name
- core.chat.prefix

I also don't quite understand what you're asking for... Just remove all the extra junk you've put in there and it should be "sorted" just fine.