lib/repo: Always look in staging directory for objects

lib/repo: Always look in staging directory for objects

Its often the case that we want to look at objects inside a commit,
before the objects the transaction is finished. For instance:
  https://github.com/flatpak/flatpak/pull/837
Which tries to verify the file permissions before committing the
transaction.

And:
  https://github.com/flatpak/flatpak/commit/1e5ffa926a25acb655af7889b679b140bf44870b
Which collects the storage size of the objects so that we can
put the total download size in the commit metadata.

I tried to find all the places where we did reads from the
object directories, and in particular this fixes:

 - `ostree_repo_load_file()` for `bare` repos (`archive` was already working).
 - `ostree_repo_query_object_storage_size()`
 - Applying deltas that reference not-yet-commited objects

Closes: #916
Approved by: cgwalters