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It appears that the reference manual (and other pdfs) are doing two things wrong.

  • They are doing what you describe.
  • They somehow logically process in such a way that when the text gets to the end of the standard page, the words beyond that (in this case, "must use the") are in a separate selection area when you select text.

Naturally in the html version all is well:

sage: sage.plot.plot.EMBEDDED_MODE = True
sage: trace('print factor(10)')
NotImplementedError: the trace command is not implemented in the Sage notebook; you must use the command line.

I'm not sure there is any way to ask Sphinx to format this correctly. This isn't exactly an answer, but hopefully will help someone else...