Disable the storage.options.pull_options.enable_partial_images option by
default, so that it will have to be explicitly enabled in order to be
used.
Update the apply-diff-from-staging-directory integration test to call
the test helper binary directly, so that the configuration file the test
writes won't have its settings overridden by command line options that
the storage() test helper function adds.
Signed-off-by: Nalin Dahyabhai <nalin@redhat.com>