It appears like that's a pipe delimited file with three columns, one of which happens to be internally delimited by commas. Use Text::CSV_XS.
use Text::CSV_XS;
my $csv = Text::CSV_XS->new( sep_char => '|' );
while ( <> ) {
$csv->parse( $_ );
my ( $file, $file_list, $yes_no ) = $csv->fields;
print "$_ $yes_no\n" for $file, split /,/, $file_list;
}
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