Cleanup two warning messages when running apidoc, and update the apidoc.gyp file to rerun the tool

utils/apidoc/apidoc.dart

 // Copyright (c) 2012, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
 /**
  * This generates the reference documentation for the core libraries that come
  * with dart. It is built on top of dartdoc, which is a general-purpose library
  * for generating docs from any Dart code. This library extends that to include
  * additional information and styling specific to our standard library.
  *
@@ skipping 98 matching lines @@
     }
   });
 
   var lister = new Directory.fromPath(doc.scriptDir.append('../../pkg')).list();
   lister.listen(
       (entity) {
         if (entity is Directory) {
           var path = new Path(entity.path);
           var libName = path.filename;
 
+          // Ignore hidden directories (like .svn) as well as pkg.xcodeproj.
+          if (libName.startsWith('.') || libName.endsWith('.xcodeproj')) {
+            return;
+          }
+
           // TODO(rnystrom): Get rid of oldStylePath support when all
           // packages are using new layout. See #5106.
           var oldStylePath = path.append('${libName}.dart');
           var newStylePath = path.append('lib/${libName}.dart');
 
           if (new File.fromPath(oldStylePath).existsSync()) {
             apidocLibraries.add(oldStylePath);
             includedLibraries.add(libName);
           } else if (new File.fromPath(newStylePath).existsSync()) {
             apidocLibraries.add(newStylePath);
@@ skipping 306 matching lines @@
     final typeName = member.owner.simpleName;
     var memberName = '$typeName.${member.simpleName}';
     if (member is MethodMirror && (member.isConstructor || member.isFactory)) {
       final separator = member.constructorName == '' ? '' : '.';
       memberName = 'new $typeName$separator${member.constructorName}';
     }
 
     return a(memberUrl(member), memberName);
   }
 }