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Flatten everything to make it easier to map command-line flags to json. The old structure was an illusion anyway because there was no mechanism to enforce that things were in the right place. This also helps with future flexibility.
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Use "file" consistently for specifying a file path. We use "filename" when adding attachments for a completely different purpose.
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The code was assuming everything was happening inside dictionaries. Instead, make the dictionary key handler creatino explicit only when iterating through dictionary keys.
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Now still have to go through and implement the handlers.
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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.