c:\@Work\Perl\monks>perl -MO=Deparse,-p -i -lpe "s/^\s*$/<r><\/r>/g"
BEGIN { $^I = ""; }
BEGIN { $/ = "\n"; $\ = "\n"; }
LINE: while (defined(($_ = <ARGV>))) {
    chomp($_);
    s[^\s*$][<r></r>]g;
}
continue {
    print($_);
}
-e syntax OK

##</code><code>##

    use constant BLANK_LINE   => qr{ \A \s* \z }xms;
    use constant EMPTY_R_PAIR => "<r></r>\n";
    ...
    $out = EMPTY_R_PAIR if $out =~ BLANK_LINE;