Use single root for nif in WriteNifTree and ResolveMissingLinkStack, to make interface consistent with the rest of niflib.

Add first vertex in match group to the head of the group, so indices are consequetive (might have a small performance benefit, and looks more like official nifs).

Provide defaults for the read values, and check for premature read failures (contributed by gentle_sal, see niftools issue #3403926).