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.