notmuch show: Preserve thread-ordering and nesting without --entire-thread

notmuch show: Preserve thread-ordering and nesting without --entire-thread

When "notmuch show" was recently modified to not show an entire thread
by default, it also lost all capability to properly order the messages
in a thread and to print their proper depth. For example, the command:

	notmuch show thread:6d5e3e276461188c5778c9f219f63782

had dramatically different output than:

	notmuch show --entire-thread thread:6d5e3e276461188c5778c9f219f63782

even though both commands were selecting and displaying the same set
of messages. The first command would diplay them "flat", (all with
depth:0), and in strict date order; while the second command would
display them "nested" (with depth based on threading), and in thread
order.

We now fix "notmuch show" without the --entire-thread option to also
display nested and thread-ordered messages.

If some messages in the thread are not included in the displayed
results, then they are not counted when computing depth values.