Move all flags to CompilerOptions (first step to stop passing the compiler to

tests/compiler/dart2js/incremental/compile_all.dart

 // Copyright (c) 2014, 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.
 
 // Helper file that can be used to manually test the stability of incremental
 // compilation.  Currently this test is not run automatically.
 
 import 'dart:async';
 
 import 'dart:io';
@@ skipping 35 matching lines @@
   CompilerImpl memoryCompiler = compilerFor(memorySourceFiles: sources);
   FormattingDiagnosticHandler handler = memoryCompiler.handler;
   handler.verbose = verbose;
   var options = ['--analyze-main'];
   if (true || verbose) options.add('--verbose');
   IncrementalCompiler compiler = new IncrementalCompiler(
       libraryRoot: memoryCompiler.libraryRoot,
       inputProvider: memoryCompiler.provider,
       outputProvider: memoryCompiler.userOutputProvider,
       diagnosticHandler: memoryCompiler.handler,
-      packageRoot: memoryCompiler.packageRoot,
+      packageRoot: memoryCompiler.options.packageRoot,
       options: options);
   Future.forEach(sources.keys, (String path) {
     UserTag.defaultTag.makeCurrent();
     if (!path.endsWith('_test.dart')) return new Future.value(null);
     testCount++;
     for (String brokenTest in brokenTests) {
       if (path.endsWith(brokenTest)) {
         print('Skipped broken test $path');
         skipCount++;
         return new Future.value(null);
@@ skipping 102 matching lines @@
     "/language/setter_declaration2_negative_test.dart",
     "/language/source_self_negative_test.dart",
     "/language/syntax_test.dart",
     "/language/type_variable_bounds2_test.dart",
     "/language/type_variable_conflict2_test.dart",
     "/language/type_variable_field_initializer_test.dart",
     "/language/type_variable_nested_test.dart",
     "/language/vm/reflect_core_vm_test.dart",
     "/language/vm/regress_14903_test.dart",
 ]);