Properly initialize the clone options

libgit2 provides an initialization function to set sane defaults. Use
that instead of setting the version by hand, as that's not the only
thing it does.

Using C.git_clone_init_options() sets the checkout strategy to SAFE,
which will checkout the files after the clone, instead of the implicit
NONE which we're setting by hand.

This fixes #425,
Use the initializer for repository init options