notmuch new: Print upgrade progress report as a percentage.

Previously we were printing a number of messages upgraded so far. The
original motivation for this was to accurately reflect the fact that
there are two passes, (so each message is processed twice and it's not
accurate to represent with a single count). But as it turns out, the
second pass takes zero time (relatively speaking) so we're still not
accounting for it.

If nothing else, the percentage-based reporting makes for a cleaner
API for the progress_notify function.