Fix several package spec bugs.

test/packages_file_test.dart

 // Copyright (c) 2015, the Dart project authors.  Please see the AUTHORS d.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 d.file.
 
 import 'descriptor.dart' as d;
 import 'test_pub.dart';
 
 main() {
   forBothPubGetAndUpgrade((command) {
     integration('.packages file is created', () {
       servePackages((builder) {
         builder.serve("foo", "1.2.3",
             deps: {'baz': '2.2.2'}, contents: [d.dir("lib", [])]);
         builder.serve("bar", "3.2.1", contents: [d.dir("lib", [])]);
         builder.serve("baz", "2.2.2",
             deps: {"bar": "3.2.1"}, contents: [d.dir("lib", [])]);
       });
 
-      d.appDir({"foo": "1.2.3"}).create();
+      d.dir(appPath, [
+        d.appPubspec({"foo": "1.2.3"}),
+        d.dir('lib')
+      ]).create();
 
       pubCommand(command);
 
       d.dir(appPath, [d.packagesFile({
-          "foo": "1.2.3", "bar": "3.2.1", "baz": "2.2.2", "myapp": "0.0.0"})])
+          "foo": "1.2.3", "bar": "3.2.1", "baz": "2.2.2", "myapp": "."})])
        .validate();
     });
 
     integration('.packages file is overwritten', () {
       servePackages((builder) {
         builder.serve("foo", "1.2.3",
             deps: {'baz': '2.2.2'}, contents: [d.dir("lib", [])]);
         builder.serve("bar", "3.2.1", contents: [d.dir("lib", [])]);
         builder.serve("baz", "2.2.2",
             deps: {"bar": "3.2.1"}, contents: [d.dir("lib", [])]);
       });
 
-      d.appDir({"foo": "1.2.3"}).create();
+      d.dir(appPath, [
+        d.appPubspec({"foo": "1.2.3"}),
+        d.dir('lib')
+      ]).create();
 
       var oldFile = d.dir(appPath, [d.packagesFile({"notFoo": "9.9.9"})]);
       oldFile.create();
       oldFile.validate();  // Sanity-check that file was created correctly.
 
       pubCommand(command);
 
       d.dir(appPath, [d.packagesFile({
-          "foo": "1.2.3", "bar": "3.2.1", "baz": "2.2.2", "myapp": "0.0.0"})])
+          "foo": "1.2.3", "bar": "3.2.1", "baz": "2.2.2", "myapp": "."})])
        .validate();
     });
 
     integration('.packages file is not created if pub command fails', () {
-      d.appDir({"foo": "1.2.3"}).create();
+      d.dir(appPath, [
+        d.appPubspec({"foo": "1.2.3"}),
+        d.dir('lib')
+      ]).create();
 
       pubCommand(command, args: ['--offline'],
                  error: "Could not find package foo in cache.\n");
 
       d.dir(appPath, [d.nothing('.packages')]).validate();
     });
 
     integration('.packages file has relative path to path dependency', () {
       servePackages((builder) {
         builder.serve("foo", "1.2.3",
             deps: {'baz': 'any'}, contents: [d.dir("lib", [])]);
         builder.serve("baz", "9.9.9",
             deps: {}, contents: [d.dir("lib", [])]);
       });
 
       d.dir("local_baz", [
         d.libDir("baz", 'baz 3.2.1'),
         d.libPubspec("baz", "3.2.1")
       ]).create();
 
       d.dir(appPath, [
         d.pubspec({
           "name": "myapp",
           "dependencies": {},
           "dependency_overrides": {
             "baz": {"path": "../local_baz"},
           }
-        })
+        }),
+        d.dir('lib')
       ]).create();
 
       pubCommand(command);
 
-      d.dir(appPath, [d.packagesFile({"myapp": "0.0.0",
-                                      "baz": "../local_baz"})]).validate();
+      d.dir(appPath, [
+        d.packagesFile({
+          "myapp": ".",
+          "baz": "../local_baz"
+        })
+      ]).validate();
     });
-
   });
 }