The main reason I don't like the mbox format is that it does not support an efficient way to skip over messages in the file.
All I'm looking for is a storage format that is line-based and has a header before each message indicating the message's size.
I could invent such a format, but I was wondering if one already existed.
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Sounds like you just need to generate an index, then, with the starting line of each of the messages. If you kept it separate, then normal mbox-reading programs could use it, and you'd have your alternate way of skipping to messages.
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I think many mail clients already do this in fact. If there is one that is likely to be used in your install, see if you can use/duplicate it's index file. (I think every client has it's own system, if they have one at all.)
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