>
> So the zip command apparently does not produce an identical compressed 
> file even if the contents are the same.
>

They never meant to be reproducible. You should use something like 
torrentzip for such purpose. 

Could .gz or .bz2 be used instead?  I think those are stable.
>

Again they never meant to be used like that, so it depends on how carefully 
you avoid any volatility. Any discrepancies in time stamps, names, paths or 
compression parameters could lead to ambiguous output.

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