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use strict;
use warnings;
...
    print encode_base64($buf);
}
close FILE;

c:\>perl encode.pl myexe.exe > mybase64.txt

use strict;
use warnings;
...

__END__
TVqQAAMAAAQAAAAAAAAAAAAAA etc. (the content of mybase64.txt)

c:\>perl2exe second_exe.pl

system("$exe_full_path -$ARGV[0]");