Copy tracked files only

This pull request adds a new VCS command to list all tracked files in a repository. When copying files, godep uses that list to make sure only tracked files are copied.

Closes #102 

I think this command `ls -R` is not going to produce output that works with `listFiles` as written below.

```
$ git ls-files
a/b
$ ls -R
a

./a:
b
```