Code looks good.  Two minor comments below.

Quoth Mark Walters on Oct 09 at  9:01 pm:
> Currently notmuch-show looks at the prefix-arg directly via
> current-prefix-arg. This changes it to use the interactive
> specification.
> ---
>  emacs/notmuch-show.el |   12 +++++++-----
>  emacs/notmuch.el      |    5 +++--
>  2 files changed, 10 insertions(+), 7 deletions(-)
> 
> diff --git a/emacs/notmuch-show.el b/emacs/notmuch-show.el
> index 5d7e24b..15f9ce6 100644
> --- a/emacs/notmuch-show.el
> +++ b/emacs/notmuch-show.el
> @@ -1080,15 +1080,17 @@ buttons for a corresponding notmuch search."
>  	(make-text-button (first link) (second link)
>  			  :type 'notmuch-button-type
>  			  'action `(lambda (arg)
> -				     (notmuch-show ,(third link)))
> +				     (notmuch-show ,(third link) current-prefix-arg))

Hmm.  Does this work?  Can you activate the button with C-u RET?

>  			  'follow-link t
>  			  'help-echo "Mouse-1, RET: search for this message"
>  			  'face goto-address-mail-face)))))
>  
>  ;;;###autoload
> -(defun notmuch-show (thread-id &optional parent-buffer query-context buffer-name)
> +(defun notmuch-show (thread-id &optional elide-toggle parent-buffer query-context buffer-name)
>    "Run \"notmuch show\" with the given thread ID and display results.
>  
> +The optional ELIDE-TOGGLE inverts the default elide behaviour.

"ELIDE-TOGGLE, if non-nil, inverts the default elide behavior."?

> +
>  The optional PARENT-BUFFER is the notmuch-search buffer from
>  which this notmuch-show command was executed, (so that the
>  next thread from that buffer can be show when done with this
> @@ -1102,7 +1104,7 @@ The optional BUFFER-NAME provides the name of the buffer in
>  which the message thread is shown. If it is nil (which occurs
>  when the command is called interactively) the argument to the
>  function is used."
> -  (interactive "sNotmuch show: ")
> +  (interactive "sNotmuch show: \nP")
>    (let ((buffer-name (generate-new-buffer-name
>  		      (or buffer-name
>  			  (concat "*notmuch-" thread-id "*")))))
> @@ -1112,9 +1114,9 @@ function is used."
>      (setq notmuch-show-process-crypto notmuch-crypto-process-mime)
>      ;; Set the default value for
>      ;; `notmuch-show-elide-non-matching-messages' in this buffer. If
> -    ;; there is a prefix argument, invert the default.
> +    ;; elide-toggle is set, invert the default.
>      (setq notmuch-show-elide-non-matching-messages notmuch-show-only-matching-messages)
> -    (if current-prefix-arg
> +    (if elide-toggle
>  	(setq notmuch-show-elide-non-matching-messages (not notmuch-show-elide-non-matching-messages)))
>  
>      (setq notmuch-show-thread-id thread-id
> diff --git a/emacs/notmuch.el b/emacs/notmuch.el
> index 0ff248b..7124d0a 100644
> --- a/emacs/notmuch.el
> +++ b/emacs/notmuch.el
> @@ -486,13 +486,14 @@ If BARE is set then do not prefix with \"thread:\""
>    "Return a list of authors for the current region"
>    (notmuch-search-properties-in-region :subject beg end))
>  
> -(defun notmuch-search-show-thread ()
> +(defun notmuch-search-show-thread (&optional elide-toggle)
>    "Display the currently selected thread."
> -  (interactive)
> +  (interactive "P")
>    (let ((thread-id (notmuch-search-find-thread-id))
>  	(subject (notmuch-search-find-subject)))
>      (if (> (length thread-id) 0)
>  	(notmuch-show thread-id
> +		      elide-toggle
>  		      (current-buffer)
>  		      notmuch-search-query-string
>  		      ;; Name the buffer based on the subject.