The problem is that use Env ... happens at compile-time, before you've stored anything in the %hash hash. Another problem is your use of qw() -- it literally sends the strings 'keys' and '%hash' to the Env module. But I think you're going about things the wrong way. Why not just place those values in the %ENV hash directly?

BEGIN {
  $ENV{APP_DIR} = "/usr/vendor/app/version";
  # etc.
}

system("printenv");  # should have the new keys in it
[download]