Bukkit

Sorry I'm not following the format, it didn't really fit the problem.
What is an orphan line?
Here is my error:
[WARNING] [YAPP] group 'user' has orphan line: == PERMISSIONS ==
[WARNING] [YAPP] group 'user' has orphan line: + essentials.tpaccept
[WARNING] [YAPP] group 'user' has orphan line: + essentials.tpa
[WARNING] [YAPP] group 'user' has orphan line: + essentials.tpdeny
[WARNING] [YAPP] group 'user' has orphan line: + essentials.tpahere
[WARNING] [YAPP] group 'user' has orphan line: + essentials.gamemode
[WARNING] [YAPP] group 'user' has orphan line: + essentials.fly
[WARNING] [YAPP] group 'user' has orphan line: + essentials.fly.safelogin
[WARNING] [YAPP] group 'user' has orphan line: + essentials.firework
[WARNING] [YAPP] group 'user' has orphan line: + essentials.firework.fire
[WARNING] [YAPP] group 'user' has orphan line: + essentials.enchant
[WARNING] [YAPP] group 'user' has orphan line: + essentials.hat
[WARNING] [YAPP] group 'user' has orphan line: + essentials.item    Allow access to the /item command.
[WARNING] [YAPP] group 'user' has orphan line: + essentials.itemspawn.item-all    If permission-based-item-spawn: Spawn all items.
[WARNING] [YAPP] group 'user' has orphan line: + essentials.oversizedstacks
[WARNING] [YAPP] group 'user' has orphan line: + essentials.enchant.allowunsafe
[INFO] YAPP data reloaded

Here is my config:
== INFORMATION ==
color : "white"
== PERMISSIONS ==
- worldedit.*
+ permissions.build
+ essentials.home
+ essentials.balance
+ essentials.pay
+ essentials.list
+ essentials.mail:
+ essentials.mail.send
+ essentials.me
+ colorportals.use
+ essentials.msg
+ essentials.sethome
+ essentials.build
+ essentials.afk
+ essentials.rules
+ essentials.help
+ essentials.recipe
+ plotme.use
+ plotme.add
+ plotme.remove
+ plotme.limit.4
+ simplespawn.use
+ simplespawn.use.default
+ simplespawn.use.world
+ simplespawn.home.set
+ simplespawn.home.use
What version of the product are you using?
1.3

I do not believe the file you've pasted is the one that it is complaining about.