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Fix typos in cli.rst
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This is used to generate a schema for the job json, which can't contain `)"` because it breaks the R"(...)" syntax in C++. While C++ accepts R"anything(...)anything" to avoid this, as of this writing, MSVC 2019 doesn't understand that. For now, just avoid it by removing parentheses from the end of short help.
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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.