repo-file: Base OstreeRepoFile on trees instead of commits

We want an OstreeRepoFile to be the way to represent a filesystem tree
inside an ostree repository. In order to do this, we need to drop the
commit from an OstreeRepoFile, and make that go to callers.

Switch all current users of ostree_repo_file_new_root to
ostree_repo_read_commit, and make the actual constructor private.

https://bugzilla.gnome.org/show_bug.cgi?id=707727
repo: Change the pairs of checksums to instead be based on OstreeRepoFiles

We want an OstreeRepoFile to be the way to reference a "filesystem
tree" that's stored in the repo, which is a combination of a DIR_TREE
and a DIR_META. The idea is that once you write an mtree to the repo
using ostree_repo_write_mtree, it becomes serialized and you get an
OstreeRepoFile in return.

Change any APIs that care about DIR_TREE / DIR_META checksums to care
about OstreeRepoFiles instead, which right now is mostly is
ostree_repo_write_commit.

https://bugzilla.gnome.org/show_bug.cgi?id=707727
repo-libarchive: Apply commit modifiers to libarchive archives as well

And document the libarchive methods as well, so we can pass a NULL
commit modifier.

https://bugzilla.gnome.org/show_bug.cgi?id=707727
repo: Make read_commit spit out a resolved commit ref as well

read_commit resolves the ref to a commit, and a lot of consumers want
the resolved commit for their own purposes; this prevents them from
calling resolve_rev themselves.

https://bugzilla.gnome.org/show_bug.cgi?id=707727
repo: Make the optimization for reusing checksums clearer

The code here is a bit hard to understand, so make it clearer by cleaning
up the flow control and adding some comments.

https://bugzilla.gnome.org/show_bug.cgi?id=707727