I have tried to put the script within a foreach loop, but it did not work.

So, I'm guessing that you didn't try it this way:

#!/usr/bin/perl
use strict;
use warnings;

for my $f ( @ARGV ) {
    local $/;
    open( I, '<', $f );
    open( O, '>', "$f.bak" );
    my $count = 0;
    my $line = <I>;

    $line =~ s{ (<\/div>) }
              { if (++$count == 2){
                  "\t<?php include(\$_SERVER['DOCUMENT_ROOT'].\"\/incl
+udes\/footer.php\"); ?>\n\n".$1;
                } else {
                  $1;
                }
              }gex;

    print O $line;
}
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That works for me. (BTW, I'm compulsive about making the indentation look right -- seems silly, but it's really helpful to keep code less illegible.)

If you have so many files that you can't fit them all as args on a command line, there's the unix "xargs" tool:

    ls | xargs your_prog   ## or use "find ... | xargs your_prog"
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