A number of material differences exist for Trees throughout the API:

Directories are uploaded individually as blobs.
Trees are fetched in a list streaming fashion from getTree
OutputDirectories are represented as digests to whole-message Trees
The digests for OutputDirectories cannot use getTree to retrieve large directories pre-parsed.
In all of these circumstances, resolving directory references throughout the tree requires computed keying of a digest, with a specific hash function, and integrity throughout (related #159)
With likely others.

For v3, we should provide a transport and storage definition for trees that resolves this bespoke treatment of trees for input/output, and meets all criteria for an efficient and tractable representations