v3 of index multiple files per msg-id, add reindex command

[David Bremner]

this obsoletes

     id:20170507124012.30188-1-david at tethera.net

As with the previous versions:

,----
| 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 last version this rebases against master (and updates
a couple of tests merged in the last month to handle the summary
format changes) and documents the summary format.