cli: make --entire-thread=false work for format=json.

The --entire-thread option in notmuch-show.c defaults to true when
format=json. Previously there was no way to turn this off. This patch
makes it respect --entire-thread=false.

To do this the patch moves the --entire-thread option to be a keyword
option using the new command line parsing to allow the existing
--entire-thread to keep working.