XSDEcoreBuilder xsdEcoreBuilder = new XSDEcoreBuilder();
		String schema = getSchemaAbsolutePath(xmlFileUri.toFileString(),
				extractSchemaLocation(xmlFileUri));
		Collection<?> eCorePackages = xsdEcoreBuilder.generate(URI
				.createFileURI(schema));

In Java application this resource is : org.eclipse.xsd.util.XSDResourceImpl
In Eclipse plug in this resource is : org.eclipse.emf.ecore.xmi.impl.EcoreResourceFactoryImpl instead.

public Collection<EObject> generate(URI uri)
  {
    ResourceSet resourceSet = createResourceSet();
    Resource [b]resource[/b]= resourceSet.getResource(uri, true);
    List<XSDSchema> xsdSchemas = new ArrayList<XSDSchema>();
    for (Object object : resource.getContents())
    {
      if (object instanceof XSDSchema)
      {
        xsdSchemas.add((XSDSchema)object);
      }
    }

    for (XSDSchema xsdSchema : xsdSchemas)
    {
      generate(xsdSchema);
    }

    List<EObject> result = new ArrayList<EObject>(targetNamespaceToEPackageMap.values());
    result.remove(XMLNamespacePackage.eINSTANCE);
    if (mapper != null)
    {
      result.add(mapper.getRoot());
    }
    return result;
  }

XsdToEcoreBuilder.generate(schemaUri, true)

 public Resource getResource(URI uri, boolean loadOnDemand)
  {
    if (resourceLocator != null)
    {
      return resourceLocator.getResource(uri, loadOnDemand);
    }

    Map<URI, Resource> map = getURIResourceMap();
    if (map != null)
    {
      Resource resource = map.get(uri);
      if (resource != null)
      {
        if (loadOnDemand && !resource.isLoaded())
        {
          demandLoadHelper(resource);
        }
        return resource;
      }
    }

    URIConverter theURIConverter = getURIConverter();
    URI normalizedURI = theURIConverter.normalize(uri);
    for (Resource resource : getResources())
    {
      if (theURIConverter.normalize(resource.getURI()).equals(normalizedURI))
      {
        if (loadOnDemand && !resource.isLoaded())
        {
          demandLoadHelper(resource);
        }

        if (map != null)
        {
          map.put(uri, resource);
        }
        return resource;
      }
    }

    Resource delegatedResource = delegatedGetResource(uri, loadOnDemand); >>>
........
  }

ResourceSetImpl.delegateGetResource(uri, loadondemand)

  
protected Resource delegatedGetResource(URI uri, boolean loadOnDemand)
  {
    EPackage ePackage = getPackageRegistry().getEPackage(uri.toString()); ||| ePackage = Test.impl.TestPackageImpl@d2b2008 (name: Test) (nsURI: file:/C:/Test.xsd, nsPrefix: Test)
    return ePackage == null ? null : ePackage.eResource(); >>>
  }

BasicEObjectImpl

  public Resource eResource()
  {
    return eInternalResource(); >>>
  }
  
>>> public Resource.Internal eInternalResource()
  {
    Resource.Internal result = eDirectResource(); >>>
...
  }

MinimalEObjectImpl

>>> public Resource.Internal eDirectResource()
  {
    return (Resource.Internal)getField(RESOURCE); >>>
  }

>>> private final Object getField(int field) <<<<<<<<<< field = 128
  {
    if (hasField(field))
    {
      int fieldIndex = fieldIndex(field);
      return fieldIndex == -1 ? eStorage : ((Object[])eStorage)[fieldIndex]; Here it return the incorrect Epackage eStorage = org.eclipse.emf.ecore.xmi.impl.EcoreResourceFactoryImpl$1@2cda5432 uri='file:/C:/Test.xsd'
  }

public Resource getResource(URI uri, boolean loadOnDemand)
  {
    ....
    Resource delegatedResource = delegatedGetResource(uri, loadOnDemand); >>>> Return delegatedResource = null
    if (delegatedResource != null)
    {
      if (map != null)
      {
        map.put(uri, delegatedResource);
      }
      return delegatedResource;
    }

    if (loadOnDemand)
    {
      Resource resource = demandCreateResource(uri);
      if (resource == null)
      {
        throw new RuntimeException("Cannot create a resource for '" + uri + "'; a registered resource factory is needed");
      }

      demandLoadHelper(resource);

      if (map != null)
      {
        map.put(uri, resource);
      }
      return resource;
    }

    return null;
  }

Nickie,

Comments below.
So you have a generated package with an nsURI that's exactly the URI of
the schema for which you're trying to generate an Ecore model. Delete
the project with that model, don't deploy it with the Eclipse
application you're trying to run, or just use that already-generated
package...