Fix up some missing consts in tree & index

Fix up some missing consts in tree & index

This fixes some missed places where we can apply const-ness to
various public APIs.

There are still some index and tree APIs that cannot take const
pointers because we sort our `git_vectors` lazily and so we can't
reliably bsearch the index and tree content without applying a
`git_vector_sort()` first.

This also fixes some missed places where size_t can be used and
where const can be applied to a couple internal functions.