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This may or may not be much help. I ran across this, this spring for a project and I used zip, not jar or COPYTOARC.
The below 2 lines was in my notes on it -

--this gets files w/o the folders structure
zip -j /tmp/myzip20.zip /tmp/mydir/*

That's really all I can tell you, I'm no zip guru.

. . .mileage may vary...
John

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