Adds config-dir as option to `cfg apply`

`push` allows a user to set a config-directory, which is great for having a staging and production environment. However, `cfg apply` does not support this same thing. This PR fixes that. 

I am in a situation where I have different configs for staging and production, but shared credentials (through `.env`). This means I need to run the command from the root, but my config files need to live in different directories (`config/production`, `config/staging`). I am actually editing my configs frequently (redirects mostly), so this adds a lot of utility for that use case.

I would love to add tests to this, but I don't know the first thing about Scala. I have just made edits to my local version of this gem in order to test (and I've been using it daily). However I have not been able to successfully build my own version of this gem because of the following error. 

```
s3_website at /Users/vox/adonit/s3_website did not have a valid gemspec.
This prevents bundler from installing bins or native extensions, but that may not affect its functionality.
The validation message from Rubygems was:
  ["resources/s3_website.jar.md5"] are not files
```

It's possible (and likely) that I'm just doing something wrong. Thanks for the gem!