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open( LIST, "mystopwords.txt" ) or die "$!";
my @stopwords = <LIST>;  # assuming one stop word per line
...

   s/\b(?:$stopregex)\b//g;

my %stopwd;
open( LIST, "my_stopwords.txt" ) or die "$!";
...

my $filtered = join '', map { exists($stopwd{$_}) ? '':$_ } split /\b/
+;