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for (sort { $module{$a} <=> $module{$b} } keys %module) {
    printf "%04d, %s\n", $module{$_}, $_;
}

/^use\s+([^\s;]+)/ && $_{$1}++ while <>;

printf "%04d, $_\n", $_{$_} for sort { $_{$b} <=> $_{$a} } keys %_;