Allow emitting output directories as plain Directory messages (#258)

* Regenerate all .pb.go files

It looks like the current ones are out of sync.

* Allow emitting output directories as plain Directory messages

As part of #257 we're discussing adding support for storing directories
in Git's format. This means OutputDirectory.tree_digest will no longer
point to an actual recursive tree object (like REv2 Tree). Instead of
doing that, I would like to investigate whether we can add native
support for storing output directories in decomposed form.