Given that you're facing a problem with tricky file names, the easiest substitute I could imagine for fixing a line of code like this:

system("program $ref_file > $outfile");
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would be to do it like this:

open( PROG, "-|", "program", $ref_file ) or die "can't launch 'program
+' on $ref_file: $!\n"

open( OUT, ">", $outfile );
while (<PROG>) {
    print OUT;
}
close PROG;
close OUT;
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That ought to take any sort of goofy file name safely in stride (for both input and output files).