There are a bunch of tests where we read or write references via the
filesystem directly. This only works with the "files" backend, but
naturally breaks if we supported any other reference format.

Refactor these tests to instead use the refdb to access those.

When testing conditional includes we overwrite the repository's config
file with the relevant conditions. This causes us to fully overwrite all
repository configuration, including the repository format version and
any extensions. While the test repository used in this test does not
have any extensions, we will add a reftable-enabled repository that does
rely on the "refStorage" extension eventually.

Fix this by only modifying the relevant config keys.

We have a bunch of checks for properties of the "files" reference
backend:

  - Whether a specific reference has been packed or whether it still
    exists as a loose reference.

  - Whether empty ref directories get pruned.

  - Whether we properly fsync data to disk.

These checks continue to be sensible for that backend, but for any other
backend they plain don't work. Adapt the tests so that we only run them
in case the repository uses the "files" backend.