Crossposted on Stackoverflow. It's polite to mention other places on the web where you asked the same question so that work doesn't get doubled.

Some notes on your post:

    $x=grep /$xrefvalue/, @xreflines;
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Instead of searching through the @xreflines like that, use instead a hash as the datastructure:

my %xreflines = map { $_ => 1 } grep /\S/, <XREF>;

...

    $x = $xreflines{ $xrefvalue };
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This removes the loop and changes it into a direct lookup whether the xref exists.

Also, for reading a (comma, or semicolon-)delimited file, consider using Text::CSV_XS instead of splitting the data yourself.