Rename private notmuch_message_t to notmuch_message_file_t

Rename private notmuch_message_t to notmuch_message_file_t

This is in preparation for a new, public notmuch_message_t.

Eventually, the public notmuch_message_t is going to grow enough
features to need to be file-backed and will likely need everything
that's now in message-file.c. So we may fold these back into one
object/implementation in the future.