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I don't think it has to be a problem directly but more how the zip file was constructed. You don't find the directory because it does not exist as a unique zip entry (where the META-INF folder for some odd reason does have one); there is only the file which happens to have a zip-entry name which to the outside world makes it appear like it is in a subdirectory.
Yes, thanks, the consensus is that the JAR file is bad, even though I created it IIRC with Java 5's zip utility.
No, the JAR file isn't bad, it's just that they aren't obliged to contain directory entries at all. They are often omitted.