[4.1] Refactor to use stores

[GrahamCampbell]

I wasn't quite happy with the last PR. // cc @KarelWintersky, @sebastiansulinski.

Changes since the last PR:

1. Dotenv\File namespace moved to Dotenv\Store\File.
2. Dotenv\Dotenv constructor final param now expects an instance of Dotenv\Store\StoreInterface or an array of paths (string[]). There are no changes to the create... static methods of Dotenv\Dotenv`.
3. Messy handling of possibly no files to read or no files could be read is now cleanly handled outside of the main dotenv class.