notmuch setup: Clean up the progress printing a bit.

Get rid of a useless leading 0 on the seconds value, and make a
distinction between "files" and "messages", (we process many
files, but not all of them are recongized as messages). Finally,
add a summary line at the end saying how many unique messages
were added to the database. Since this comes right after the
total number of files, it gives the user at least a hint as
to how many messages were encountered with duplicate message IDs.