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I'd say moving unknown files to a temporary folder is the best solution.
As for writing metadata to an OPF file, that can be done, but I would suggest making it optional as it entails a performance penalty. Once its implemented we can decide if the performance penalty is severe enough to warrant it being default off or on. Also as Starson pointed out, currently the code for writing custom column metadata to OPF files is non-existant.
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