In analysis server, favor package root setting over ".packages" file.

pkg/analysis_server/test/context_manager_test.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.
 
 library test.context.directory.manager;
 
 import 'dart:collection';
 
 import 'package:analysis_server/src/context_manager.dart';
 import 'package:analyzer/file_system/file_system.dart';
@@ skipping 562 matching lines @@
 
     // smoketest resolution
     SourceFactory sourceFactory = callbacks.currentContext.sourceFactory;
     Source resolvedSource =
         sourceFactory.resolveUri(source, 'package:unittest/unittest.dart');
     expect(resolvedSource, isNotNull);
     expect(resolvedSource.fullName,
         equals('/home/somebody/.pub/cache/unittest-0.9.9/lib/unittest.dart'));
   }
 
+  void test_setRoots_addFolderWithPackagespecAndPackageRoot() {
+    // The package root should take priority.
+    String packagespecPath = posix.join(projPath, '.packages');
+    resourceProvider.newFile(packagespecPath,
+        'unittest:file:///home/somebody/.pub/cache/unittest-0.9.9/lib/');
+    String packageRootPath = '/package/root/';
+    manager.setRoots(<String>[projPath], <String>[],
+        <String, String>{projPath: packageRootPath});
+    expect(callbacks.currentContextPaths, hasLength(1));
+    expect(callbacks.currentContextPaths, contains(projPath));
+    expect(callbacks.currentContextDispositions[projPath].packageRoot,
+        packageRootPath);
+  }
+
   void test_setRoots_addFolderWithPubspec() {
     String pubspecPath = posix.join(projPath, 'pubspec.yaml');
     resourceProvider.newFile(pubspecPath, 'pubspec');
     manager.setRoots(<String>[projPath], <String>[], <String, String>{});
     // verify
     expect(callbacks.currentContextPaths, hasLength(1));
     expect(callbacks.currentContextPaths, contains(projPath));
     expect(callbacks.currentContextFilePaths[projPath], hasLength(0));
   }
 
@@ skipping 1062 matching lines @@
 class TestUriResolver extends UriResolver {
   Map<Uri, Source> uriMap;
 
   TestUriResolver(this.uriMap);
 
   @override
   Source resolveAbsolute(Uri uri, [Uri actualUri]) {
     return uriMap[uri];
   }
 }