Rick Rankin writes:
 -   (format "\\(%s\\|%s\\)\\'"
 +   (format "\\(%s\\|%s\\)"
            shell-prompt-pattern tramp-shell-prompt-pattern)))
 
 Can anyone tell me if that extra apostrophe actually belongs there
 and if so, why? I don't see how it could work unless you're prompt
 actually ends with an apostrophe. 
It's intentional.  Specifically, it's not an apostrophe.  The
backslash makes it a special regular expression operator that matches
the empty string at end-of-buffer.
The intention is to match only at the last prompt in the buffer.
Evidently your remote shell is producing text that matches what TRAMP
considers to be a shell prompt, and then adding something to it.  The
"expected" way to fix this is to
(setq tramp-shell-prompt-pattern
      (concat tramp-shell-prompt-pattern re-matching-trailing-stuff))
or alternatively teach the shell not to do that.
Could you show us and the TRAMP developers what the "extra" stuff that
your remote shell is appending looks like?
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