I don't want to obfuscate filenames in recipe downloads as I often look at the downloaded files to debug problems and the nice folder structure makes it easy to find files.
And I tried FBReader on my computer, it works fine. Only Sigil has issues and I'm sure if you point them out to Valloric on the Sigil forum they will be quickly fixed.
That said, I would be willing to accept the patch if you can make it optional. That way when developing recipes it would use the current structure, but for normal downloads, it would not.
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