Several Small Changes

* allow vender.headers_dir to be an array
* added back App.configs for BubbleWrap dependency
* fixed order of operations in option parsing
* ignore copy of hidden directories (example: .svn) in resource copy.
* add configuration_build_dir to vender setting

I was originally planning on giving each change as a separate branch, but it because too hard for me to maintain and due to other things that would break in my specific huge vendor project and a Cocao Pods dependency, I couldn't validate my build worked unless ALL these changes where in.
Trying to tease them out into separate branches would have burnt away too much time.

Let me know if you really really really need them separately and I see what I can do.

Look at the commit comments to figure out the changes. 

This also include the patch-1 I submitted a couple days ago, so you can ignore that one.