I don't know about your full disk (I actually never used CGI), but there are a few things you may want to change:
- You should either use autodie or check the return value of open.
- You probably meant s/</&lt;/g
- m< /domain.com$ >x will match "/domain/com", "/domainacom" ... (See quotemeta)
- You could do only one while loop with the flip flop operator:

while(<IN>)
{
  next if 1../The mail system/; # The condition will be true from line
+ 1 until "The mail system"
  # Code here
}
[download]

Edit: and having two nested loop with $_ as a loop variable doesn't help readability. Besides, while does not localize $_, so you are actually changing the content of the @files array every time you read a line (each element of @files is aliased to $_, and you write a line in $_).

Edit again: and just to prove what I'm saying:

use v5.14;
use Data::Dumper;
my @list = 1..3;

for (@list)
{
  print while (<DATA>);
}

say Dumper \@list;
__DATA__
[download]

$VAR1 = [
          undef,
          undef,
          undef
        ];
[download]

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