Cleanup docblocks

* Standardize on 2 spaces for indentation. That's what is used in MRI
docblocks and also what correctly works in both YARDoc and RDoc.
* Enclosing text in "`" characters has no meaning, use "+" instead.
* Fix some other small typos.
More docs for the Index class.
More docs for Index.
More Index docs.
Put call-seq: on the second docblock line.
Fix a typo.
Fix rendering issues in the Repository#reset docs.
Add missing call sequences and re-word a bit.
Switch this around.
Docs for Index.new.
Add Docs for Branch#head? and some other tiny cleanups.
Fix docs for Reference.valid_name?.
Cleanup and extend Reference docs.
Cleanup docs for Rugged::Branch.
Cleanup Rugged::Config docs.
Minor cleanups in the Rugged::Commit docs.
Align the docs a bit more.
Add some more missing docs.
Fix docs for Rugged::Object.rev_parse_oid.
Add docs for Rugged::Repository.bare.