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I use Calibre for PC, not Mac, but as far as I know the Mac version works the same way. If so, it will work perfectly with your Paperwhite and doesn't require that to jailbreak or modify your Kindle in any way.
I'm not a fan of Kindle collections or of any of Amazon's limited options for organizing and sorting my library and use Calibre exclusively for both Amazon and non-Amazon ebooks.
Once you've installed Calibre on your computer and configured it using their set up wizard, you need to decide whether you want to install the Apprentice Alf plug-ins. If so, you need to do it before adding books to your Cailbre library since the plug ins only work when adding books to the library, not on books previously added.
I set up user defined columns for genres, read/un-read, etc., and have hidden the preconfigured columns I don't use (ratings, etc). There are numerous forum posts, tutorials and articles that explain how to customize Calibre. You can find them with a Google search.
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