Try setting the working directory explicitly.

utils/pub/git_source.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 git_source;
 
 import 'git.dart' as git;
 import 'io.dart';
 import 'package.dart';
 import 'source.dart';
@@ skipping 135 matching lines @@
    * If [mirror] is true, create a bare, mirrored clone. This doesn't check out
    * the working tree, but instead makes the repository a local mirror of the
    * remote repository. See the manpage for `git clone` for more information.
    */
   Future _clone(String from, String to, {bool mirror: false}) {
     // Git on Windows does not seem to automatically create the destination
     // directory.
     return ensureDir(to).chain((_) {
       var args = ["clone", from, to];
       if (mirror) args.insertRange(1, 1, "--mirror");
-      return git.run(args);
+      return git.run(args, workingDir: currentWorkingDir);
     }).transform((result) => null);
   }
 
   /**
    * Checks out the reference [ref] in [repoPath].
    */
   Future _checkOut(String repoPath, String ref) {
     return git.run(["checkout", ref], workingDir: repoPath).transform(
         (result) => null);
   }
@@ skipping 50 matching lines @@
 
   /**
    * Returns [description] if it's a description, or [PackageId.description] if
    * it's a [PackageId].
    */
   _getDescription(description) {
     if (description is PackageId) return description.description;
     return description;
   }
 }