This looks like a great solution to a fairly common and annoying problem. I do have a question, though. If the user thinks the file and index are out of sync, (s)he can recreate the index. No problem there. But what happens if some other process diddles with the file? Or rather, what would protect the file, once it's created?
I could see some other program writing to the file, unaware of its special status, and trashing the relationship with the index. If then a user relies on the index, bad things could happen. Perhaps a sort of sanity check (modification times match)?
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