dirty working tree with existing Godeps file

I went to try out the new save functionality on an existing repo with an existing `Godeps` file from an older `godep` release and encountered the following:

```bash
[~/dev/src/github.com/bitly/nsq](master)$ godep save ./...
godep: dirty working tree: /Users/mreiferson/dev/src/github.com/bitly/nsq/util
godep: error loading dependencies
```

I don't have `github.com/bitly/nsq/util` as part of the exiting `Godeps` file because it's part of the repository and doesn't need to be pinned.

What's happening is that the `save` command begins by deleting any existing `Godeps` file, which is checked into vcs, thus "dirtying" the working tree when `godep` checks `isDirty` for any *local* dependencies.  `isDirty` uses diff under the hood, so I experimented with the following patch to be more specific about what it wants diffed:

```diff
diff --git a/vcs.go b/vcs.go
index 4ce568c..b5260ee 100644
--- a/vcs.go
+++ b/vcs.go
@@ -42,7 +42,7 @@ var vcsGit = &VCS{
 
        IdentifyCmd: "rev-parse HEAD",
        DescribeCmd: "describe --tags",
-       DiffCmd:     "diff {rev}",
+       DiffCmd:     "diff {rev} .",
 
        CreateCmd:   "init --bare",
        LinkCmd:     "remote add {remote} {url}",
```

I can open a PR taking this approach if you agree with the solution (obviously applying the fix to all the supported vcs).