Just try some print(tm)-debugging:

my ($cmd, $chdir) = split(';',$run[$element],2);
[download]

becomes

print '@run:', join ', ', @run, "\n";
print "\$element: $element\n";
my ($cmd, $chdir) = split(';',$run[$element],2);
print "\$cmd: $cmd\n";
print "\$chdir: $chdir\n";
[download]

You'll be surprised when you discover how many problems you can solve on your own using this technique.