Use pub list-package-dirs in analyzer command line

pkg/analyzer/lib/options.dart

 // Copyright (c) 2013, 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.
 
 library options;
 
 import 'dart:io';
 
 import 'package:args/args.dart';
 
@@ skipping 100 matching lines @@
     return options;
   }
 
   static CommandLineOptions _parse(List<String> args) {
     args = args.expand((String arg) => arg.split('=')).toList();
     var parser = new _CommandLineParser()
       ..addFlag('batch', abbr: 'b', help: 'Run in batch mode',
           defaultsTo: false, negatable: false)
       ..addOption('dart-sdk', help: 'The path to the Dart SDK')
       ..addOption('package-root', abbr: 'p',
-          help: 'The path to the package root')
+          help: 'The path to the package root. The flag package-root is deprecated. Remove to use package information computed by pub.')
       ..addOption('format',
           help: 'Specifies the format in which errors are displayed')
       ..addFlag('machine',
           help: 'Print errors in a format suitable for parsing (deprecated)',
           defaultsTo: false, negatable: false)
       ..addFlag('version', help: 'Print the analyzer version',
           defaultsTo: false, negatable: false)
       ..addFlag('no-hints', help: 'Do not show hint results',
           defaultsTo: false, negatable: false)
       ..addFlag('ignore-unrecognized-flags',
@@ skipping 198 matching lines @@
 
   _getNextFlagIndex(args, i) {
     for ( ; i < args.length; ++i) {
       if (args[i].startsWith('--')) {
         return i;
       }
     }
     return i;
   }
 }