If you use system in the following fashion you don't need to worry about quotes, shell vars etc.. being interpreted by Perl.

@args=qw(command arg1 arg2);
system(@args);
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Oh, and on testing not by the shell either

~$ perl -e '@args=qw(echo Hello;echo World);system(@args);'
Hello;echo World
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So it prevents this form of abuse by default, I wasn't aware of that feature at all. Thanks