Added clean_state_files
Proper naming
Added docs
Added sphinx rtd theme
Fix sphinx complaints about the docs

Use the right namespace so Refspec and TransferProgress show up. These
classes are not instantiated by the user, so they were not promoted to
the pygit2 module. Use autoclass so it lists everything for us.

Also use autoclass for the reflog. We had a difference is oid vs id
between the docs and the code.
Move Index to cffi

This commit gives us feature-parity with the version in C.
Add looking up conflicts in an Index
Move merge tests to their own file

The method is in Repository, but the merge functionality is separate. We
will introduce more tests in this area later.
Add tests for Index conflict access
Add documentation for conflicts and fixup Index

Add documentation for the conflicts, and add some for IndexEntry and
Index which went missing during the conversion to cffi.
Support del in ConflictCollection
Make python3 happy
Merge remote-tracking branch 'carlos/doc-fixup'
Merge remote-tracking branch 'vtemian/sphinx'
Merge remote-tracking branch 'carlos/cffi-index'
checkout: move the code to cffi

As part of this, make the strategy part of **kwargs, in preparation for
supporting more options.
checkout: add support for overriding the target directory
Cleanup a little bit the code
Update the README for libgit2's change in master branch

Provide instructions to use the release, rather than the master branch,
which is now where development happens.
Merge remote-tracking branch 'vtemian/more-pep8'