clone: refactor to pass clone options around

Instead of dealing with the clone options sub-options (fetch, checkout,
etc) individually, treat them as a cohesive whole when passing them
throughout the system.

Additionally, move some functions around within the file to avoid
unnecessary decls at the top of the file.  And change a function
signature to avoid conflating truth with error.

include/git2/checkout.h

@@ -189,7 +189,7 @@ typedef enum {
 	*/
 	GIT_CHECKOUT_NONE = (1u << 30),
 
-	/**
+	/*
 	 * THE FOLLOWING OPTIONS ARE NOT YET IMPLEMENTED
 	 */