cli: move show to the new --exclude= option naming scheme.

cli: move show to the new --exclude= option naming scheme.

This moves notmuch show to the --exclude=(true|false) naming
scheme. When exclude=false show returns all threads that match
including those that only match in an excluded message. The excluded
messages are flagged.

When exclude=true the behaviour depends on whether --entire-thread is
set. If it is not set then show only returns the messages which match
and are not excluded. If it is set then show returns all messages in
the threads that match in a non-excluded message, flagging the excluded
messages in these threads. The rationale is that it is awkward to use
a thread with some missing messages.