v2 of index multiple files per msg-id, add reindex command

[David Bremner]

This obsoletes id:20170414025004.5334-1-david at tethera.net. Let me
repeat the warning from that version:

,----
| WARNING: reindexing is an intrusive operation. I don't think this will
| corrupt your database, but previous versions thrashed threading pretty
| well. notmuch-dump is your friend.
`----

Compared to the previous version, this one cleans up the code to print
total file counts (splitting into multiple commits), and updates doc
and tests.

There is a lot of code movement here, mainly splitting up database.cc

d