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Why? The main methods that create them return smart pointers so that users can initialize them when needed, which you can't do with references. Returning pointers instead of references makes for a more uniform interface.
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Use named functions rather than just end() for clarity.
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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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Handle optional choices in addition to required choices. Refactor the way help options are added to completion to make it work with optional help choices.