A problem seen with an ear that has a lib/shared.jar entry, but which as explicitly excluded this jar from the ear classpath by specifying an empty library-directory:
<?xml version="1.0" encoding="UTF-8"?>
<application xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="5" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/application_5.xsd">
<module>
<java>ejb3_assembly_librarydirectory_disable_client.jar</java>
</module>
<module>
<ejb>ejb3_assembly_librarydirectory_disable_ejb.jar</ejb>
</module>
<library-directory></library-directory>
</application>

fails to deploy because one of the shared.jar classes is referenced by some annotation:
14:36:20,139 WARN [HackClassloaderMetaDataDeployer] FIXME Using loader repository config: jboss.j2ee:service=EARDeployment,url='ejb3_assembly_librarydirectory_disable.ear',extension=LoaderRepository for vfszip:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear use classloading metadata not loader repository config
14:36:20,194 ERROR [AbstractKernelController] Error installing to PostClassLoader: name=vfszip:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear state=ClassLoader mode=Manual requiredState=PostClassLoader
org.jboss.deployers.spi.DeploymentException: Cannot process metadata
at org.jboss.deployers.spi.DeploymentException.rethrowAsDeploymentException(DeploymentException.java:49)
at org.jboss.deployment.AnnotationMetaDataDeployer.deploy(AnnotationMetaDataDeployer.java:181)
at org.jboss.deployment.AnnotationMetaDataDeployer.deploy(AnnotationMetaDataDeployer.java:93)
at org.jboss.deployers.plugins.deployers.DeployerWrapper.deploy(DeployerWrapper.java:169)
at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:970)
at org.jboss.deployers.plugins.deployers.DeployersImpl.install(DeployersImpl.java:911)
at org.jboss.dependency.plugins.AbstractControllerContext.install(AbstractControllerContext.java:348)
at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:1522)
at org.jboss.dependency.plugins.AbstractController.incrementState(AbstractController.java:898)
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1026)
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:948)
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:786)
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:519)
at org.jboss.deployers.plugins.deployers.DeployersImpl.process(DeployersImpl.java:594)
at org.jboss.deployers.plugins.main.MainDeployerImpl.process(MainDeployerImpl.java:541)
at org.jboss.deployment.services.DeploymentManagerService.deploy_phase2(DeploymentManagerService.java:412)
at org.jboss.deployment.services.DeploymentManagerService.deploy(DeploymentManagerService.java:295)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:157)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:96)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:668)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.jboss.jmx.connector.invoker.InvokerAdaptorService.invoke(InvokerAdaptorService.java:270)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:157)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:96)
at org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java:138)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:90)
at org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOperationInterceptor.java:140)
at org.jboss.jmx.connector.invoker.SerializableInterceptor.invoke(SerializableInterceptor.java:74)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:90)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:668)
at org.jboss.invocation.jrmp.server.JRMPProxyFactory.invoke(JRMPProxyFactory.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:157)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:96)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:668)
at org.jboss.invocation.jrmp.server.JRMPInvoker$MBeanServerAction.invoke(JRMPInvoker.java:815)
at org.jboss.invocation.jrmp.server.JRMPInvoker.invoke(JRMPInvoker.java:416)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
at sun.rmi.transport.Transport$1.run(Transport.java:153)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:466)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:707)
at java.lang.Thread.run(Thread.java:613)
Caused by: java.lang.RuntimeException: java.lang.ClassNotFoundException: com.sun.ts.tests.ejb30.assembly.librarydirectory.disable.AssemblyBean from BaseClassLoader@dfd3f2{VFSClassLoaderPolicy@d3f467{name=vfszip:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear domain=ClassLoaderDomain@e68009{name=jboss.j2ee:extension=LoaderRepository,service=EARDeployment,url='ejb3_assembly_librarydirectory_disable.ear' parentPolicy=AFTER_BUT_JAVA_BEFORE parent=ClassLoaderDomain@201ee4{DefaultDomain}} roots=[MemoryContextHandler@5417105[path= context=vfsmemory://5c4o0b-6i47u9-fkegg4nk-1-fkegvjjg-1o real=vfsmemory://5c4o0b-6i47u9-fkegg4nk-1-fkegvjjg-1o], DelegatingHandler@12116064[path=ejb3_assembly_librarydirectory_disable_client.jar context=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear real=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear/ejb3_assembly_librarydirectory_disable_client.jar], DelegatingHandler@9617413[path=ejb3_assembly_librarydirectory_disable_ejb.jar context=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear real=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear/ejb3_assembly_librarydirectory_disable_ejb.jar], DelegatingHandler@8168644[path= context=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear real=vfszip:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear]] delegates=null exported=[com.sun.ts.tests.ejb30.assembly.librarydirectory.disable, com.sun.ts.lib.harness, lib.shared.jar.com.sun.ts.tests.ejb30.assembly.librarydirectory.disable, lib.shared.jar.META-INF, META-INF, lib.shared.jar.com.sun.ts.tests.ejb30.assembly.common, com.sun.ts.tests.ejb30.common.helper, lib.shared.jar.com.sun.ts.tests.ejb30.common.helper, com.sun.ts.tests.ejb30.assembly.common] <IMPORT-ALL>NON_EMPTY}}
at org.jboss.deployers.plugins.annotations.WeakClassLoaderHolder.loadClass(WeakClassLoaderHolder.java:76)
at org.jboss.deployers.plugins.annotations.AbstractElement.getOwner(AbstractElement.java:73)
at org.jboss.deployment.OptAnnotationMetaDataDeployer.getClasses(OptAnnotationMetaDataDeployer.java:170)
at org.jboss.deployment.OptAnnotationMetaDataDeployer.processJBossMetaData(OptAnnotationMetaDataDeployer.java:131)
at org.jboss.deployment.OptAnnotationMetaDataDeployer.processMetaData(OptAnnotationMetaDataDeployer.java:83)
at org.jboss.deployment.AnnotationMetaDataDeployer.deploy(AnnotationMetaDataDeployer.java:177)
... 65 more
Caused by: java.lang.ClassNotFoundException: com.sun.ts.tests.ejb30.assembly.librarydirectory.disable.AssemblyBean from BaseClassLoader@dfd3f2{VFSClassLoaderPolicy@d3f467{name=vfszip:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear domain=ClassLoaderDomain@e68009{name=jboss.j2ee:extension=LoaderRepository,service=EARDeployment,url='ejb3_assembly_librarydirectory_disable.ear' parentPolicy=AFTER_BUT_JAVA_BEFORE parent=ClassLoaderDomain@201ee4{DefaultDomain}} roots=[MemoryContextHandler@5417105[path= context=vfsmemory://5c4o0b-6i47u9-fkegg4nk-1-fkegvjjg-1o real=vfsmemory://5c4o0b-6i47u9-fkegg4nk-1-fkegvjjg-1o], DelegatingHandler@12116064[path=ejb3_assembly_librarydirectory_disable_client.jar context=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear real=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear/ejb3_assembly_librarydirectory_disable_client.jar], DelegatingHandler@9617413[path=ejb3_assembly_librarydirectory_disable_ejb.jar context=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear real=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear/ejb3_assembly_librarydirectory_disable_ejb.jar], DelegatingHandler@8168644[path= context=file:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear real=vfszip:/Users/svn/JBossHead/jboss-head/build/output/jboss-5.0.0.CR2/server/cts/tmp/jsr88/ejb3_assembly_librarydirectory_disable.ear]] delegates=null exported=[com.sun.ts.tests.ejb30.assembly.librarydirectory.disable, com.sun.ts.lib.harness, lib.shared.jar.com.sun.ts.tests.ejb30.assembly.librarydirectory.disable, lib.shared.jar.META-INF, META-INF, lib.shared.jar.com.sun.ts.tests.ejb30.assembly.common, com.sun.ts.tests.ejb30.common.helper, lib.shared.jar.com.sun.ts.tests.ejb30.common.helper, com.sun.ts.tests.ejb30.assembly.common] <IMPORT-ALL>NON_EMPTY}}
at org.jboss.classloader.spi.base.BaseClassLoader.loadClass(BaseClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:242)
at org.jboss.deployers.plugins.annotations.WeakClassLoaderHolder.loadClass(WeakClassLoaderHolder.java:72)

... 70 more