Cleanup docblocks

This PR contains changes to make the Rugged documentation shine. :sparkles: 

* [x] Standardize on 2 spaces for indentation in C docblocks. That's what is used in MRI
docblocks and also what correctly works in both YARDoc and RDoc.
* [x] Add documentation for all methods of `Rugged::Index`.
* [x] Go over all classes / methods and add missing documentation.