#!/usr/bin/perl

while ( <> ) {
    $fn = 1 if /^\@footnote:/;
    if ( $fn ) {
      ( s/^\[(\d+)\] (.*)// ) && ( $footer->{ $fn_hash->{ $1 } } = sprintf "%s", $2 ) || print;
   } else {
      while ( s/^(.*?)\[(\d+)\]//x ) {
         printf "%s[%s]", $1, $fn_hash->{ $2 } ||= ++$index;
      }
      print;
   } 
}

foreach ( sort keys %$footer ) {
   printf "[%s] %s\n", $_, $footer->{ $_ };
}