new: Enhance progress reporting

notmuch new reports progress only during the "first" phase when the
files on disk are traversed and indexed. After this phase, other
operations like rename detection and maildir flags synchronization are
performed, but the user is not informed about them. Since these
operations can take significant time, we want to inform the user about
them.

This patch enhances the progress reporting facility that was already
present. The timer that triggers reporting is not stopped after the
first phase but continues to run until all operations are finished. The
rename detection and maildir flag synchronization are enhanced to report
their progress.