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This is caused by --sequesterRsrc option. I think this option was added to preserve the executable flags on the main program.
--sequesterRsrc
When creating a PKZip archive, preserve resource forks and HFS meta-data in the subdirectory __MACOSX. PKZip extraction will automatically find
these resources.
The zip file when unpack contains the following directories:
Cyberduck.app
__MACOSX
The __MACOSX folder should not be distributed (not required)
Can be deleted once unpacked and it doesn't affect the application operations.
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