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my @to_be_sorted;
foreach my $filename (@filelist) {
...
     my ($major, $minor, $third) = split /\./, $version;
     push @to_be_sorted,  [$filename, $root, $major, $minor, $third];
}

0  ARRAY(0x600500678)
      0  'bar_123.10.0_deb'
...
      2  123
      3  10
      4  0

my @sorted_array = map {$_->[0]} 
                   sort { $a->[1] cmp $b->[1] 
...
                       || $a->[3] <=> $b->[3] 
                       || $a->[4] <=> $b->[4] }
                   @to_be_sorted;