loader: Do not include content of nested trees
Previously the loader was raising an error when encountering a nested tree (inventory entry of kind 'tree-reference').
Those nested trees are typically created from git submodules when importing a bazaar repository from a git one.
By default bazaar does not recurse on a nested tree content when exporting a revision and simply creates an empty directory instead.
So adopt the same behavior in the loader as it exists cases where a nested tree cannot be resolved.
Related to #4583.