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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