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I would advise stepping through 4.5.x
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Why?
I"m not saying I won't do it (although I'd rather not), I'm just wondering if there is something in the upgrade process that I've missed. All the reading I've done in the upgrade documentation indicates that it should be OK to go from 4.0.3 to 5.0.2 in one fell swoop.
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do you hit this even on a tiny jump to 4.0.5_GA_518.UBUNTU6 etc?
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I probably would have hit the same error, since it was caused by the file system corruption, and fsck incorrectly deciding that a file should really be a directory.