inconsistent handling of stderr in notmuch-emacs

[David Bremner]

Rob noticed that generating extra output on stderr from the notmuch cli
breaks some things in notmuch-emacs (in his case this was from a wrapper
script).

notmuch-search seems fairly robust at this point, but at least
notmuch-hello and notmuch-mua-mail get confused by the extra
output. I guess this is because of code calling #'call-process without
specifying something to do with stderr.

I don't know how often this is problem, but I guess it would be nice to
eventually only call notmuch using make-process (for recent enough
emacs). This allows cleaner handling of stderr.