cli: omit excluded messages in results where appropriate.

cli: omit excluded messages in results where appropriate.

In all cases of notmuch count/search/show where the results returned
cannot reflect the exclude flag return just the matched not-excluded
results. If the caller wishes to have all the matched results (i.e.,
including the excluded ones) they should call with the
--no-exclude option.

The relevant cases are
    count: both threads and messages
    search: all cases except the summary view
    show: mbox format