runtime descriptor: runtime modeler error: Wrapper class es.ua.itm.jaxws.Run is not found. Have you run APT to generate them?

El siguiente error se crea cuando la librería JAXB 2.1 no se incluye en el proyecto por DELANTE de JAX-WS 2.1.

SEVERE: Exception sending context initialized event to listener instance of class com.sun.xml.ws.transport.http.servlet.WSServletContextListener
com.sun.xml.ws.transport.http.servlet.WSServletException: WSSERVLET11: failed to parse runtime descriptor: runtime modeler error: Wrapper class es.ua.itm.jaxws.Run is not found. Have you run APT to generate them?
at com.sun.xml.ws.transport.http.servlet.WSServletContextListener.contextInitialized(WSServletContextListener.java:118)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3843)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4350)
at org.apache.catalina.startup.HostConfig.checkResources(HostConfig.java:1114)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1212)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:293)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1337)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1601)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1610)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1590)
at java.lang.Thread.run(Thread.java:619)

[wsimport] Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3

El siguiente error me ha aparecido nada más volver de vacaciones, sin razón aparente:

[wsimport] Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3
[wsimport] at com.sun.org.apache.xml.internal.resolver.readers.TextCatalogReader.nextToken(TextCatalogReader.java:249)
[wsimport] at com.sun.org.apache.xml.internal.resolver.readers.TR9401CatalogReader.readCatalog(TR9401CatalogReader.java:81)
[wsimport] at com.sun.org.apache.xml.internal.resolver.Catalog.parseCatalog(Catalog.java:680)
[wsimport] at com.sun.xml.ws.util.xml.XmlUtil.createEntityResolver(XmlUtil.java:222)
[wsimport] at com.sun.tools.ws.wscompile.WsimportOptions.parseArguments(WsimportOptions.java:140)
[wsimport] at com.sun.tools.ws.wscompile.Options.parseArguments(Options.java:225)
[wsimport] at com.sun.tools.ws.wscompile.WsimportTool.run(WsimportTool.java:154)
[wsimport] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[wsimport] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[wsimport] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[wsimport] at java.lang.reflect.Method.invoke(Method.java:597)
[wsimport] at com.sun.tools.ws.Invoker.invoke(Invoker.java:116)
[wsimport] at com.sun.tools.ws.WsImport.main(WsImport.java:52)

BUILD FAILED
/home/jmgomez/Documents/Projects/intime/nbproject/jaxws-build.xml:59: wsimport failed

Lo he solucionado eliminando la referencia al web service que tenía en la aplicación (update.xml) y volviéndola a crear. La razón por la que me ha aparecido este error me parece que es porque modifiqué el build.xml, porque hago la referencia en otro proyecto y éste funciona perfectamente.