[MERGE REVIEW] Use InventoryDirectory to represent tree root

[Aaron Bentley]

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Hi all,

Here's another hopefully-uncontroversial patch split out from the
nested-trees branch.  Michael Ellerman's Shelf plugin was invaluable for
this work.

It uses InventoryDirectory to represent root entries, rather than
RootEntry, which is now deprecated.  This means that the inventory kind
of a root entry is 'directory', not 'root_directory'.

Inventory.is_root is provided to determine whether an inventory id is
the root inventory id, instead of checking the file kind.

Aaron
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