Add support for 1+ configuration directories.

Problem/Motivation

When using Acquia Site Studio, its generally a best practice to keep its configuration in a seperate directory (ex. config/sitestudio). Config Patch assumes only one base directory, which prevents this from exporting any Site Studio related changes as part of the patch list.

Steps to reproduce

Proposed resolution

Add support for more than one directory.

Remaining tasks

User interface changes

API changes

Data model changes