Fixes relative templates specified in `apm init`

When a relative path to a set of templates was specified, `apm init` would output directories from the `/`.

So

```
cd ~/github
git clone git@github.com:atom/space-pen-example-templates.git
apm init -p my-package-name --template space-pen-example-templates/templates
```

The output is like

```
Users
|__ben
   |__github
      |__keymaps
...
```