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This is a massive rewrite of the help text and cli.rst section of the manual. All command-line flags now have their own help and are specifically index. qpdf --help is completely redone.
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The agogo theme doesn't do very well on narrow screens. The code blocks were used for shell commands but were using Python syntax highlighting.
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These are for ancient versions.
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This was inserted by sphinx-quickstart, but it doesn't do anything for us.
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Pandoc doesn't convert <xref> correctly, but it does so consistently, so this commit just changes all xref links to :ref:.