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.

This started as a complex new test for checkout going through the
"typechanges" test repository, but that revealed numerous issues
with checkout, including:

* complete failure with submodules
* failure to create blobs with exec bits
* problems when replacing a tree with a blob because the tree
  "example/" sorts after the blob "example" so the delete was
  being processed after the single file blob was created

This fixes most of those problems and includes a number of other
minor changes that made it easier to do that, including improving
the TYPECHANGE support in diff/status, etc.

Returning a negative cancels the walk, and returning a positive one
causes us to skip an entry, which was previously done by a negative
value.

This allows us to stay consistent with the rest of the functions that
take a callback and keeps the skipping functionality.

Conflicts:
	src/notes.c
	src/transports/git.c
	src/transports/http.c
	src/transports/local.c
	tests-clar/odb/foreach.c