Program: 51098
Project: 51098
Buggy source:
private void initialize(BeanManager manager){
  if (!lookupExtensionInBeanManager) {
    try {
      InitialContext ic=InitialContextHelper.getInitialContext();
      if (ic != null) {
        ic.rebind(JNDI_CDIEXTENSION_NAME,this);
      }
    }
 catch (    NamingException ex) {
      throw new RuntimeException(ex);
    }
  }
  Set<Class<? extends Annotation>> set=new HashSet<Class<? extends Annotation>>();
  set.add(CookieParam.class);
  set.add(FormParam.class);
  set.add(HeaderParam.class);
  set.add(MatrixParam.class);
  set.add(PathParam.class);
  set.add(QueryParam.class);
  set.add(Context.class);
  knownParameterQualifiers=Collections.unmodifiableSet(set);
  Map<Class<? extends Annotation>,Parameter.Source> map=new HashMap<Class<? extends Annotation>,Parameter.Source>();
  map.put(CookieParam.class,Parameter.Source.COOKIE);
  map.put(FormParam.class,Parameter.Source.FORM);
  map.put(HeaderParam.class,Parameter.Source.HEADER);
  map.put(MatrixParam.class,Parameter.Source.MATRIX);
  map.put(PathParam.class,Parameter.Source.PATH);
  map.put(QueryParam.class,Parameter.Source.QUERY);
  map.put(Context.class,Parameter.Source.CONTEXT);
  paramQualifiersMap=Collections.unmodifiableMap(map);
  Set<Class<?>> set3=new HashSet<Class<?>>();
  set3.add(Application.class);
  set3.add(HttpHeaders.class);
  set3.add(Providers.class);
  set3.add(Request.class);
  set3.add(SecurityContext.class);
  set3.add(UriInfo.class);
  set3.add(ExceptionMapperContext.class);
  set3.add(ExtendedUriInfo.class);
  set3.add(FeaturesAndProperties.class);
  set3.add(HttpContext.class);
  set3.add(HttpRequestContext.class);
  set3.add(HttpResponseContext.class);
  set3.add(MessageBodyWorkers.class);
  set3.add(ResourceContext.class);
  set3.add(WebApplication.class);
  staticallyDefinedContextBeans=Collections.unmodifiableSet(set3);
  Map<Class<? extends Annotation>,Set<DiscoveredParameter>> map2=new HashMap<Class<? extends Annotation>,Set<DiscoveredParameter>>();
  for (  Class<? extends Annotation> qualifier : knownParameterQualifiers) {
    map2.put(qualifier,new HashSet<DiscoveredParameter>());
  }
  discoveredParameterMap=Collections.unmodifiableMap(map2);
  syntheticQualifierMap=new HashMap<DiscoveredParameter,SyntheticQualifier>();
  toBeInitializedLater=new ArrayList<InitializedLater>();
}

Fixed version (ground truth):
private void initialize(BeanManager manager){
  if (!lookupExtensionInBeanManager) {
    try {
      InitialContext ic=InitialContextHelper.getInitialContext();
      if (ic != null) {
        javax.naming.Context jerseyConfigJNDIContext=createJerseyConfigJNDIContext(ic);
        jerseyConfigJNDIContext.rebind(JNDI_CDIEXTENSION_NAME,this);
      }
    }
 catch (    NamingException ex) {
      throw new RuntimeException(ex);
    }
  }
  Set<Class<? extends Annotation>> set=new HashSet<Class<? extends Annotation>>();
  set.add(CookieParam.class);
  set.add(FormParam.class);
  set.add(HeaderParam.class);
  set.add(MatrixParam.class);
  set.add(PathParam.class);
  set.add(QueryParam.class);
  set.add(Context.class);
  knownParameterQualifiers=Collections.unmodifiableSet(set);
  Map<Class<? extends Annotation>,Parameter.Source> map=new HashMap<Class<? extends Annotation>,Parameter.Source>();
  map.put(CookieParam.class,Parameter.Source.COOKIE);
  map.put(FormParam.class,Parameter.Source.FORM);
  map.put(HeaderParam.class,Parameter.Source.HEADER);
  map.put(MatrixParam.class,Parameter.Source.MATRIX);
  map.put(PathParam.class,Parameter.Source.PATH);
  map.put(QueryParam.class,Parameter.Source.QUERY);
  map.put(Context.class,Parameter.Source.CONTEXT);
  paramQualifiersMap=Collections.unmodifiableMap(map);
  Set<Class<?>> set3=new HashSet<Class<?>>();
  set3.add(Application.class);
  set3.add(HttpHeaders.class);
  set3.add(Providers.class);
  set3.add(Request.class);
  set3.add(SecurityContext.class);
  set3.add(UriInfo.class);
  set3.add(ExceptionMapperContext.class);
  set3.add(ExtendedUriInfo.class);
  set3.add(FeaturesAndProperties.class);
  set3.add(HttpContext.class);
  set3.add(HttpRequestContext.class);
  set3.add(HttpResponseContext.class);
  set3.add(MessageBodyWorkers.class);
  set3.add(ResourceContext.class);
  set3.add(WebApplication.class);
  staticallyDefinedContextBeans=Collections.unmodifiableSet(set3);
  Map<Class<? extends Annotation>,Set<DiscoveredParameter>> map2=new HashMap<Class<? extends Annotation>,Set<DiscoveredParameter>>();
  for (  Class<? extends Annotation> qualifier : knownParameterQualifiers) {
    map2.put(qualifier,new HashSet<DiscoveredParameter>());
  }
  discoveredParameterMap=Collections.unmodifiableMap(map2);
  syntheticQualifierMap=new HashMap<DiscoveredParameter,SyntheticQualifier>();
  toBeInitializedLater=new ArrayList<InitializedLater>();
}