Delete the packages/ directory before installing new packages to it.

utils/pub/entrypoint.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.
 
 #library('entrypoint');
 
 #import('io.dart');
 #import('lock_file.dart');
 #import('package.dart');
 #import('root_source.dart');
@@ skipping 119 matching lines @@
     return _loadLockFile().chain((lockFile) {
       var versionSolver = new VersionSolver(cache.sources, root, lockFile);
       for (var dependency in dependencies) {
         versionSolver.useLatestVersion(dependency);
       }
       return versionSolver.solve();
     }).chain(_installDependencies);
   }
 
   /**
-   * Installs all dependencies listed in [packageVersions] and writes a
-   * [LockFile].
+   * Removes the old packages directory, installs all dependencies listed in
+   * [packageVersions], and writes a [LockFile].
    */
   Future _installDependencies(List<PackageId> packageVersions) {
-    return _removeUnusedDependencies(packageVersions).chain((_) {
+    return cleanDir(path).chain((_) {
       return Futures.wait(packageVersions.map((id) {
         if (id.source is RootSource) return new Future.immediate(id);
         return install(id);
       }));
     }).chain(_saveLockFile)
       .chain(_installSelfReference)
       .chain(_linkSecondaryPackageDirs);
   }
 
   /**
@@ skipping 20 matching lines @@
 
       return true;
     });
 
     future.then((text) =>
         completer.complete(new LockFile.parse(text, cache.sources)));
     return completer.future;
   }
 
   /**
-   * Removes all dependencies that are no longer depended on from the `packages`
-   * directory. [packageIds] is a list of all packages that are still depended
-   * on.
-   */
-  Future _removeUnusedDependencies(List<PackageId> packageIds) {
-    var dependenciesToKeep = packageIds.map((id) => id.name);
-
-    return dirExists(path).chain((exists) {
-      if (exists) return listDir(path);
-      return new Future.immediate([]);
-    }).chain((existingDependencies) {
-      existingDependencies = existingDependencies.map(basename);
-      var dependenciesToRemove =
-          new List.from(setMinus(existingDependencies, dependenciesToKeep));
-      return Futures.wait(dependenciesToRemove.map((dependency) {
-        return deleteDir(join(path, dependency));
-      }));
-    });
-  }
-
-  /**
    * Saves a list of concrete package versions to the `pubspec.lock` file.
    */
   Future _saveLockFile(List<PackageId> packageIds) {
     var lockFile = new LockFile.empty();
     for (var id in packageIds) {
       if (id.source is! RootSource) lockFile.packages[id.name] = id;
     }
 
     return writeTextFile(join(root.dir, 'pubspec.lock'), lockFile.serialize());
   }
@@ skipping 74 matching lines @@
    * Creates a symlink to the `packages` directory in [dir] if none exists.
    */
   Future _linkSecondaryPackageDir(String dir) {
     var to = join(dir, 'packages');
     return exists(to).chain((exists) {
       if (exists) return new Future.immediate(null);
       return createSymlink(path, to);
     });
   }
 }