rose app-upgrade, rose macro: fix relative opts.conf_dir

#1161 broke most relative `--config`, `-C` usage for
`rose app-upgrade` and `rose macro`. This wasn't
picked up because it happens to work for the usage
in the test-battery. The current behaviour is actually
to create a new relative path from the actual
app directory, which is pretty bad.

@matthewrmshin, please review.