Comment 11 for bug 1126349

Follow up to my previous comment (#10), i just looked through the .log file some more and i'm pretty sure what i said is exactly what is happening. I told the server to shut down, so it starts telling the plugins to shut down

j com.untamedears.realisticbiomes.persist.PlantManager.saveAllAndStop()V+4
j com.untamedears.realisticbiomes.RealisticBiomes.onDisable()V+23

and then it tries to load the class from the jar, and then it calls the zip code (which ended up crashing) , probably cause the zip/jar file is different then when it was first loaded, due to me overwriting it.

J java.util.zip.ZipFile.getEntry(J[BZ)J
J java.util.jar.JarFile.getEntry(Ljava/lang/String;)Ljava/util/zip/ZipEntry;
J sun.misc.URLClassPath.getResource(Ljava/lang/String;Z)Lsun/misc/Resource;
J java.net.URLClassLoader$1.run()Ljava/lang/Object;
v ~StubRoutines::call_stub
J java.security.AccessController.doPrivileged(Ljava/security/PrivilegedExceptionAction;Ljava/security/AccessControlContext;)Ljava/lang/Object;
J java.net.URLClassLoader.findClass(Ljava/lang/String;)Ljava/lang/Class;
j org.bukkit.plugin.java.PluginClassLoader.findClass0(Ljava/lang/String;Z)Ljava/lang/Class;+85
j org.bukkit.plugin.java.JavaPluginLoader.getClassByName0(Ljava/lang/String;)Ljava/lang/Class;+93
j org.bukkit.plugin.java.PluginClassLoader.findClass0(Ljava/lang/String;Z)Ljava/lang/Class;+75
j org.bukkit.plugin.java.PluginClassLoader.findClass(Ljava/lang/String;)Ljava/lang/Class;+19
j java.lang.ClassLoader.loadClass(Ljava/lang/String;Z)Ljava/lang/Class;+70
j java.lang.ClassLoader.loadClass(Ljava/lang/String;)Ljava/lang/Class;+3
v ~StubRoutines::call_stub