notmuch_database_close: Explicitly flush the Xapian database.

This would have helped with the recent bug causing "notmuch new"
to not record any results in the database. I'm not sure why
the explicit flush would be required, (shouldn't the destructor
always ensure that things flush?), but perhaps some outstanding
references from the leak prevented that.

In any case, an explicit flush on close() seems to make sense.