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,

pygit2/__init__.py

@@ -151,6 +151,9 @@ def clone_repository(
     d['callback'] = credentials
     d_handle = ffi.new_handle(d)
 
+    # Perform the initialization with the version we compiled
+    C.git_clone_init_options(opts, C.GIT_CLONE_OPTIONS_VERSION)
+
     # We need to keep the ref alive ourselves
     checkout_branch_ref = None
     if branch:
@@ -160,11 +163,8 @@ def clone_repository(
     remote_name_ref = ffi.new('char []', to_bytes(remote_name))
     opts.remote_name = remote_name_ref
 
-    opts.version = 1
     opts.ignore_cert_errors = ignore_cert_errors
     opts.bare = bare
-    opts.remote_callbacks.version = 1
-    opts.checkout_opts.version = 1
     if credentials:
         opts.remote_callbacks.credentials = _credentials_cb
         opts.remote_callbacks.payload = d_handle

pygit2/decl.h

@@ -353,6 +353,9 @@ typedef struct git_clone_options {
 	git_signature *signature;
 } git_clone_options;
 
+#define GIT_CLONE_OPTIONS_VERSION ...
+int git_clone_init_options(git_clone_options *opts, unsigned int version);
+
 int git_clone(git_repository **out,
 	const char *url,
 	const char *local_path,