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I have Emacs run in daemon mode at system startup, and run emacsclient automatically when I login to X. I also recently started running midnight-mode, which regularly runs clean-buffer-list, which wants to kill the buffer showing my home folder since I rarely visit it. This is a problem because that buffer is associated with the emacsclient invocation, so killing it closes all my frames.

Is there a way to decouple emacsclient from that particular buffer? I have to run emacsclient on something in order for it to open a window, so I give it $HOME.

Alternatively, is there a way to get clean-buffer-list to look at server-buffer-clients and skip buffers with it set?

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Oddly enough, clean-buffer-list doesn't directly offer a convenient hook for that, no. But I think you can get the behavior you're asking for with a hack like:

(defun my-midnight-hack (orig-fun buffer)
  (with-current-buffer buffer
    (if server-buffer-clients
         ;; Return the current time, to pretend it's in use.
         (float-time)
      (funcall orig-fun buffer))))
(advice-add 'midnight-buffer-display-time :around #'my-midnight-hack)

Another approach would be to run emacsclient -n ... so that emacsclient immediately returns and killing that buffer should then not kill all your frames (because the buffer is not marked as belonging to an emacsclient).

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