When deploying an Applicatin that brings its own JSF Implementation, JBoss reads the correct jars after providing jboss-deployment-structure.xml but the AnnotationProvider fails to initialize with a NoSuchMethodException. I believe that it is related to this post: http://community.jboss.org/message/621225

09:52:20,870 INFO [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Mojarra 2.0.3 (FCS b03) für Kontext '/frameevolution-admin' wird initialisiert.
09:52:22,495 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/jsf-impl-2.0.3-FCS.jar/com/sun/faces/jsf-ri-runtime.xml
09:52:22,495 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/frame-ui-web-layout-9.0.0-20111109.013036-36.jar/META-INF/faces-config.xml
09:52:22,526 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [31ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/jsf-facelets-1.1.15.jar/META-INF/faces-config.xml
09:52:22,526 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/richfaces-impl-jsf2-3.3.3.Final.jar/META-INF/faces-config.xml
09:52:22,526 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/richfaces-impl-jsf2-3.3.3.Final.jar/META-INF/ajax-context.faces-config.xml
09:52:22,526 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/richfaces-ui-3.3.3.Final.jar/META-INF/faces-config.xml
09:52:22,526 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse vfs:/D:/apps/jboss-eap-6.0/standalone/deployments/frameevolution-sf-ear.ear/frameevolution-sf-admin-web.war/WEB-INF/lib/spring-faces-2.1.1.RELEASE.jar/META-INF/faces-config.xml
09:52:22,526 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : Parse jndi:/default-host/frameevolution-admin/WEB-INF/faces-config.xml
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Starting sort pass number 1...
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Comparing ,
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Comparing ,
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Comparing ,
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Comparing ,
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Comparing ,
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Comparing ,
09:52:22,542 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [0ms] : "faces-config" document sorting complete in 1.
09:52:22,557 FEIN [javax.enterprise.resource.webcontainer.jsf.application] (MSC service thread 1-4) java.lang.NoSuchMethodException: org.jboss.as.web.deployment.jsf.JandexAnnotationProvider.<init>(javax.servlet.ServletContext, com.sun.faces.spi.AnnotationProvider): java.lang.NoSuchMethodException: org.jboss.as.web.deployment.jsf.JandexAnnotationProvider.<init>(javax.servlet.ServletContext, com.sun.faces.spi.AnnotationProvider)
at java.lang.Class.getConstructor0(Class.java:2706) [:1.6.0_24]
at java.lang.Class.getDeclaredConstructor(Class.java:1985) [:1.6.0_24]
at com.sun.faces.spi.ServiceFactoryUtils.getProviderFromEntry(ServiceFactory.java:79) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.spi.AnnotationProviderFactory.createAnnotationProvider(AnnotationProviderFactory.java:66) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigManager$AnnotationScanTask.<init>(ConfigManager.java:746) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigManager.initialize(ConfigManager.java:324) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigureListener.contextInitialized(ConfigureListener.java:220) [jsf-impl-2.0.3-FCS.jar:]
at org.apache.catalina.core.StandardContext.contextListenerStart(StandardContext.java:3392) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3850) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.as.web.deployment.WebDeploymentService.start(WebDeploymentService.java:77) [jboss-as-web-7.1.0.Alpha1-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1824)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1759)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [:1.6.0_24]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [:1.6.0_24]
at java.lang.Thread.run(Thread.java:662) [:1.6.0_24]

09:52:22,557 INFO [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Unsanitized stacktrace from failed start...: javax.faces.FacesException: Class org.jboss.as.web.deployment.jsf.JandexAnnotationProvider is not an instance of com.sun.faces.spi.AnnotationProvider
at com.sun.faces.spi.AnnotationProviderFactory.createAnnotationProvider(AnnotationProviderFactory.java:74) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigManager$AnnotationScanTask.<init>(ConfigManager.java:746) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigManager.initialize(ConfigManager.java:324) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigureListener.contextInitialized(ConfigureListener.java:220) [jsf-impl-2.0.3-FCS.jar:]
at org.apache.catalina.core.StandardContext.contextListenerStart(StandardContext.java:3392) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3850) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.as.web.deployment.WebDeploymentService.start(WebDeploymentService.java:77) [jboss-as-web-7.1.0.Alpha1-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1824)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1759)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [:1.6.0_24]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [:1.6.0_24]
at java.lang.Thread.run(Thread.java:662) [:1.6.0_24]

09:52:22,557 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Mojarra (2.0.3 (FCS b03)) für Kontext ''

'' wurde initialisiert.
09:52:22,557 FEIN [javax.enterprise.resource.webcontainer.jsf.timing] (MSC service thread 1-4) [TIMING] - [1734ms] : Initialization of context /frameevolution-admin
09:52:22,557 ERROR [org.apache.catalina.core.ContainerBase.[jboss.web].[default-host].[/frameevolution-admin]] (MSC service thread 1-4) Exception sending context initialized event to listener instance of class com.sun.faces.config.ConfigureListener: com.sun.faces.config.ConfigurationException: CONFIGURATION FAILED! Class org.jboss.as.web.deployment.jsf.JandexAnnotationProvider is not an instance of com.sun.faces.spi.AnnotationProvider
at com.sun.faces.config.ConfigManager.initialize(ConfigManager.java:351) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigureListener.contextInitialized(ConfigureListener.java:220) [jsf-impl-2.0.3-FCS.jar:]
at org.apache.catalina.core.StandardContext.contextListenerStart(StandardContext.java:3392) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3850) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.as.web.deployment.WebDeploymentService.start(WebDeploymentService.java:77) [jboss-as-web-7.1.0.Alpha1-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1824)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1759)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [:1.6.0_24]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [:1.6.0_24]
at java.lang.Thread.run(Thread.java:662) [:1.6.0_24]
Caused by: javax.faces.FacesException: Class org.jboss.as.web.deployment.jsf.JandexAnnotationProvider is not an instance of com.sun.faces.spi.AnnotationProvider
at com.sun.faces.spi.AnnotationProviderFactory.createAnnotationProvider(AnnotationProviderFactory.java:74) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigManager$AnnotationScanTask.<init>(ConfigManager.java:746) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigManager.initialize(ConfigManager.java:324) [jsf-impl-2.0.3-FCS.jar:]
... 9 more

09:52:22,557 ERROR [org.apache.catalina.core.StandardContext] (MSC service thread 1-4) Error listenerStart
09:52:22,557 ERROR [org.apache.catalina.core.StandardContext] (MSC service thread 1-4) Context [/frameevolution-admin] startup failed due to previous errors
09:52:22,557 DEBUG [org.apache.catalina.core.ContainerBase.[jboss.web].[default-host].[/frameevolution-admin]] (MSC service thread 1-4) Stopping filters
09:52:22,557 DEBUG [org.apache.catalina.session.ManagerBase] (MSC service thread 1-4) Unloading persisted sessions
09:52:22,557 DEBUG [org.apache.catalina.core.StandardContext] (MSC service thread 1-4) Sending application stop events
09:52:22,557 FEIN [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) ConfigureListener.contextDestroyed(frameevolution-sf-admin-web)
09:52:22,557 SCHWERWIEGEND [javax.enterprise.resource.webcontainer.jsf.config] (MSC service thread 1-4) Unexpected exception when attempting to tear down the Mojarra runtime: java.lang.IllegalStateException: Die Anwendung wurde bei Systemstart nicht einwandfrei initialisiert, Factory konnte nicht gefunden werden: javax.faces.application.ApplicationFactory
at javax.faces.FactoryFinder$FactoryManager.getFactory(FactoryFinder.java:800) [jsf-api-2.0.3-FCS.jar:]
at javax.faces.FactoryFinder.getFactory(FactoryFinder.java:302) [jsf-api-2.0.3-FCS.jar:]
at com.sun.faces.config.InitFacesContext.getApplication(InitFacesContext.java:104) [jsf-impl-2.0.3-FCS.jar:]
at com.sun.faces.config.ConfigureListener.contextDestroyed(ConfigureListener.java:312) [jsf-impl-2.0.3-FCS.jar:]
at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:3489) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.apache.catalina.core.StandardContext.stop(StandardContext.java:3999) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3917) [jbossweb-7.0.3.Final-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.as.web.deployment.WebDeploymentService.start(WebDeploymentService.java:77) [jboss-as-web-7.1.0.Alpha1-redhat-1.jar:7.1.0.Alpha1-redhat-1]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1824)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1759)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [:1.6.0_24]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [:1.6.0_24]
at java.lang.Thread.run(Thread.java:662) [:1.6.0_24]

09:52:22,557 INFO [org.apache.catalina.core.ContainerBase.[jboss.web].[default-host].[/frameevolution-admin]] (MSC service thread 1-4) Closing Spring root WebApplicationContext