Set `UnixMode` NodeProperty on root of merged merkle tree

buildbox-run-userchroot, due to it using it's namesake userchroot, requires that the top level directory have not-fully open permissions, at most 0755. Since other runners don't have this restriction, it should communicate that through the use of a NodeProperty on the top level Directory message. It can do this as a final step after merging the chrootRootDigest with the input_root, before staging it. This would allow us to drop buildbox-casd's current behavior of setting 0755 permissions for ALL stage directories and go back to using 0777.

See buildbox-casd#44 (closed) for more background on this issue.