lib: Separate list of all messages from top-level messages

Previously, thread.cc built up a list of all messages, then
proceeded to tear it apart to transform it into a list of
top-level messages.  Now we simply build a new list of top-level
messages.

This simplifies the interface to _notmuch_message_add_reply,
eliminates the pointer acrobatics from
_resolve_thread_relationships, and will enable us to do things
with the list of all messages in the following patches.