lib/checkout: For "process whiteouts" mode, replace directories too

lib/checkout: For "process whiteouts" mode, replace directories too

I'm playing around with some ostree ⇔ OCI/Docker bits, and ran
into this while importing an OCI image that built from the Fedora
base image where `/home` is a regular directory, and I added a layer
that did the ostree bits of moving it to `/var` and leaving a symlink.

OCI/Docker supports this.  Now since "process whiteouts" is really the
"enable OCI/Docker" mode, let's only replace dirs if that's enabled.
This leaves the `UNION_FILES` targeted for its original use case
which is unioning components/packages.  (Although that use case itself
is now a bit superceded by `UNION_IDENTICAL`, but eh).

Closes: #1294
Approved by: jlebon