main method:

 public static void main(String[] args) throws Exception
{
    if (args.length != EXPECTED_NUMBER_OF_ARGUMENTS)
    {
        System.err.println("Usage - java XFRCompiler ConfigXML PackageXML XFR");
    }

    String configXML = args[0];
    String packageXML = args[1];
    String xfr = args[2];

    AutoConfigCompiler compiler = new AutoConfigCompiler();
    compiler.setConfigDocument(loadDocument(configXML));
    compiler.setPackageInfoDoc(loadDocument(packageXML));
    // compiler.setVisiblityDoc(loadDocument("VisibilityFilter.xml"));
    compiler.compileModel(xfr);     

}

private static Document loadDocument(String fileName) throws Exception
{
    TXDOMParser parser = (TXDOMParser) ParserFactory.makeParser(TXDOMParser.class.getName());
    InputSource source = new InputSource(new FileInputStream(fileName));
    parser.parse(source);
    return parser.getDocument();  

}

testcase:

@Test
public void testCompileModel() throws Exception
{
  // construct parameters
  URL configFile =   Thread.currentThread().getContextClassLoader().getResource("Ford_2008_Mustang_Config.xml");
  URL packageFile = Thread.currentThread().getContextClassLoader().getResource("Ford_2008_Mustang_Package.xml");
  File tmpFile = new File("Ford_2008_Mustang_tmp.xfr");
  if(!tmpFile.exists()) {
     tmpFile.createNewFile();
  }

  String[] args = new     String[]{configFile.getPath(),packageFile.getPath(),tmpFile.getPath()};

  try {
    // test main method
    XFRCompiler.main(args);
  } catch (Exception e) {
    assertTrue(true);
  }
  try {
    // test args length is less than 3
    XFRCompiler.main(new String[]{"",""});
  } catch (Exception e) {  
    assertTrue(true);
  }
  tmpFile.delete(); 
}

Coverage outputs displayed as the lines from String configXML = args[0]; in main method are not covered.