Did it stop working after an OSX update? As I mentioned in another reply, MacOS X plays games like this.

The actual epub file is probably in that directory somewhere, so you will need to improve your Perl script to check if the "file" that it has been asked to copy is actually a directory (the -d file test operator should help here) and, if so, search within to locate the actual file and copy the real file and not the Apple "file".

In reply to Re^3: 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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