Something

#!/usr/bin/perl

use warnings;
use strict;

foreach my $file (<*.php>) {
  open FILE, ">$file" or die "$!";
  while (<FILE>) {
    s/foot\.php/\.\/include\/foot\.php/; 
    s/head\.php/\.\/include\/head\.php/; 
    print FILE;
  }
  close FILE or die "$!";
}