Presumably, a "local Apache web site" is a directory in the filesystem somewhere? As choroba mentioned, Perl should not be magically unpacking ZIP archives while copying them.

Is "'ls'" the system ls command, examining that local directory that Apache is serving files from?

Check your Apache configuration: are you using some kind of module that magically translates ZIP archives to directories?

There is some kind of magic that has been set up here that needs to be dispelled. Can you post the Perl code that copies the files, preferably as an update to your post?

In reply to Re: copy an epub as a file, not a directory by jcb
in thread copy an epub as a file, not a directory by Trudge

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