Server Severe errors.... Cannot figure this out... tried everything.

Code:

08:51:10 [INFO] Preparing spawn area: 16%
08:51:11 [INFO] Preparing spawn area: 20%
08:51:12 [INFO] Preparing spawn area: 24%
08:51:14 [INFO] Preparing spawn area: 24%
08:51:15 [INFO] Preparing spawn area: 28%
08:51:16 [INFO] Preparing spawn area: 28%
08:51:17 [INFO] Preparing spawn area: 32%
08:51:18 [INFO] Preparing spawn area: 36%
08:51:19 [INFO] Preparing spawn area: 40%
08:51:20 [INFO] Preparing spawn area: 44%
08:51:21 [INFO] Preparing spawn area: 44%
08:51:22 [INFO] Preparing spawn area: 52%
08:51:23 [INFO] Preparing spawn area: 52%
08:51:24 [INFO] Preparing spawn area: 56%
08:51:25 [INFO] Preparing spawn area: 57%
08:51:26 [INFO] Preparing spawn area: 61%
08:51:28 [INFO] Preparing spawn area: 65%
08:51:30 [INFO] Preparing spawn area: 69%
08:51:31 [INFO] Preparing spawn area: 73%
08:51:32 [INFO] Preparing spawn area: 81%
08:51:33 [INFO] Preparing spawn area: 81%
08:51:35 [INFO] Preparing spawn area: 85%
08:51:36 [INFO] Preparing spawn area: 89%
08:51:37 [INFO] Preparing spawn area: 97%
08:51:38 [INFO] Preparing spawn area: 97%
08:51:38 [INFO] [Inception] version 0.9delta is enabled!
08:51:38 [INFO] LWC     Loaded 134 locale strings (0 overrides)
08:51:38 [INFO] [Permissions] (Yeti) disabled successfully.
08:51:38 [SEVERE] Error occurred while enabling LWC v3.11 (Is it up to date?): c
om/nijikokun/bukkit/Permissions/Permissions
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at com.griefcraft.lwc.LWC.load(Unknown Source)
        at com.griefcraft.lwc.LWCPlugin.onEnable(Unknown Source)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
Caused by: java.lang.ClassNotFoundException: com.nijikokun.bukkit.Permissions.Pe
rmissions
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:36)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:24)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 12 more
08:51:38 [INFO] MCMACOMPAT r14
08:51:38 [INFO] McMyAdmin Compatibility Plugin version r14 started.
08:51:38 [SEVERE] Error occurred while enabling MultiVerse v1.7.2 (Is it up to d
ate?): com/nijikokun/bukkit/Permissions/Permissions
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at com.onarandombox.Rigby.MultiVerse.MultiVerse.checkPermissions(MultiVe
rse.java:514)
        at com.onarandombox.Rigby.MultiVerse.MultiVerse.onEnable(MultiVerse.java
:75)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
Caused by: java.lang.ClassNotFoundException: com.nijikokun.bukkit.Permissions.Pe
rmissions
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:36)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:24)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 12 more
08:51:38 [INFO] [MYHOME]: 5 homes loaded
08:51:38 [INFO] [MYHOME] Permissions enabled using: Permissions v3.1.6
08:51:38 [WARNING] [MYHOME] 'Help' isn't detected. No /help support.
08:51:38 [INFO] [MYHOME] MyHome 1.9.5 enabled
08:51:38 [INFO] [Permissions] SQL Interface enabled!
08:51:38 [INFO] [StarterKit] Enabled
08:51:38 [INFO] [Permissions] (Yeti) disabled successfully.
08:51:38 [SEVERE] Could not pass event PLUGIN_ENABLE to MultiVerse
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at com.onarandombox.Rigby.MultiVerse.MVPluginListener.onPluginEnable(MVP
luginListener.java:21)
        at org.bukkit.plugin.java.JavaPluginLoader$41.execute(JavaPluginLoader.j
ava:527)
        at org.bukkit.plugin.RegisteredListener.callEvent(RegisteredListener.jav
a:58)
        at org.bukkit.plugin.SimplePluginManager.callEvent(SimplePluginManager.j
ava:321)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:864)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at com.nilla.vanishnopickup.VanishNoPickup.setupPermissions(VanishNoPick
up.java:115)
        at com.nilla.vanishnopickup.VanishNoPickup.onEnable(VanishNoPickup.java:
69)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
Caused by: java.lang.ClassNotFoundException: com.nijikokun.bukkit.Permissions.Pe
rmissions
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:36)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:24)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 18 more
08:51:38 [SEVERE] Error occurred while enabling VanishNoPickup v1.9.9 (Is it up
to date?): com/nijikokun/bukkit/Permissions/Permissions
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at com.nilla.vanishnopickup.VanishNoPickup.setupPermissions(VanishNoPick
up.java:116)
        at com.nilla.vanishnopickup.VanishNoPickup.onEnable(VanishNoPickup.java:
69)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
Caused by: java.lang.ClassNotFoundException: com.nijikokun.bukkit.Permissions.Pe
rmissions
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:36)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:24)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 12 more
08:51:38 [INFO] WorldEdit 4.6 enabled.
08:51:38 [INFO] WorldEdit: No known permissions plugin detected. Using configura
tion file for permissions.
08:51:38 [INFO] [xWarp]: No Register found. Deactivating Register support.
08:51:38 [INFO] [xWarp]: 3 warps loaded
08:51:38 [WARNING] [xWarp]: 3 invalid warps found.
08:51:38 [WARNING] [xWarp]: Skiped disabled permissions system: Permissions v3.1
.6
08:51:38 [INFO] [xWarp]: No permissions system found until here. A permissions p
lugin will be maybe activated later.
08:51:38 [INFO] [xWarp]: No economy system found until here. A economy plugin wi
ll be maybe activated later.
08:51:38 [INFO] [xWarp]: xWarp 2.12.0 enabled
08:51:38 [INFO] [Citizens] Loaded 0 quests.
08:51:38 [INFO] [Citizens] Permissions enabled.
08:51:38 [INFO] [Citizens] version [1.0.9] (Odyssey) loaded
08:51:38 [INFO] [Permissions] (Yeti) disabled successfully.
08:51:38 [INFO] WorldEdit: No known permissions plugin detected. Using configura
tion file for permissions.
08:51:38 [WARNING] [xWarp]: Skiped disabled permissions system: Permissions v3.1
.6
08:51:38 [INFO] WorldEdit: No known permissions plugin detected. Using configura
tion file for permissions.
08:51:38 [SEVERE] Could not pass event PLUGIN_ENABLE to MultiVerse
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at com.onarandombox.Rigby.MultiVerse.MVPluginListener.onPluginEnable(MVP
luginListener.java:21)
        at org.bukkit.plugin.java.JavaPluginLoader$41.execute(JavaPluginLoader.j
ava:527)
        at org.bukkit.plugin.RegisteredListener.callEvent(RegisteredListener.jav
a:58)
        at org.bukkit.plugin.SimplePluginManager.callEvent(SimplePluginManager.j
ava:321)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:864)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.dynmap.permissions.NijikokunPermissions.create(NijikokunPermissio
ns.java:19)
        at org.dynmap.DynmapPlugin.onEnable(DynmapPlugin.java:71)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
08:51:38 [SEVERE] Error occurred while enabling dynmap v0.19.1 (Is it up to date
?): com/nijikokun/bukkit/Permissions/Permissions
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at org.dynmap.permissions.NijikokunPermissions.<init>(NijikokunPermissio
ns.java:25)
        at org.dynmap.permissions.NijikokunPermissions.create(NijikokunPermissio
ns.java:20)
        at org.dynmap.DynmapPlugin.onEnable(DynmapPlugin.java:71)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
Caused by: java.lang.ClassNotFoundException: com.nijikokun.bukkit.Permissions.Pe
rmissions
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:36)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:24)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 13 more
08:51:38 [INFO] [Factions v1.3.5] === INIT START ===
08:51:38 [INFO] [Factions v1.3.5] Loading conf from disk
08:51:38 [INFO] [Factions v1.3.5] Loading players from disk
08:51:38 [INFO] [Factions v1.3.5] Loading factions from disk
08:51:38 [WARNING] [Factions v1.3.5] Stored location's world "vanilla" not found
 on server; dropping the location.
08:51:38 [INFO] [Factions v1.3.5] Loading board from disk
08:51:38 [SEVERE] Error occurred while enabling Factions v1.3.5 (Is it up to dat
e?): com/nijikokun/bukkit/Permissions/Permissions
java.lang.NoClassDefFoundError: com/nijikokun/bukkit/Permissions/Permissions
        at org.mcteam.factions.Factions.setupPermissions(Factions.java:175)
        at org.mcteam.factions.Factions.onEnable(Factions.java:120)
        at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:126)
        at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader
.java:857)
        at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManage
r.java:264)
        at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:151)
        at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:136
)
        at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:284)
        at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:271)
        at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:148)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
Caused by: java.lang.ClassNotFoundException: com.nijikokun.bukkit.Permissions.Pe
rmissions
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:36)
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.
java:24)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 12 more
08:51:38 [INFO] Done (3.275s)! For help, type "help" or "?"
08:51:38 [INFO] [Citizens] Loaded 0 NPCs.
>

 

Those exceptions are being caused because a number of plugins can not find the Permissions plugin, or at least not active one. You seem to have one, but it keeps disabling itself. You might want to check that it is up to date

 

Remove Permissions and any other bridges and download the latest version (3.1.6 at time of writing).