Hiding cryptographic keys is apparently quite a difficult thing to do. I am told by people who know about these things that locating cryptographic keys is actually really easy - you just look for areas in your file/disk with very high entropy - which will either be compressed files, encrypted files, or keys.
However, the fundimental flaw in your system is that perl itself needs to be able to read your source files somehow. Once you allow that, there are any number of techniques to allow someone to read it.
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