Me? I worry about those global variables like $file, $html, %CONFIG and %REPLACEMENTS and find myself wondering if it wouldn't be better to make them attributes of the parser object:

sub ParserClass::do_global_replace {
    my $self = shift;
    while (my $token = $self->get_token) {
        $self->maybe_do_replacement($token);
    }
    return $self
}

sub ParserClass::maybe_do_replacement {
    my $self  = shift;
    my $token = shift;

    if ($self->stack_matched) {
        $self->append_replacement_html;
    }
    else {
        $self->append_html($token);
    }
    return $self
}

sub ParserClass::append_replacement_html {
    my $self = shift;
    $self->append_html($self->replacement_html);
    $self->increment_replacement_count;
}
[download]

(Admittedly, some of the utility functions are left as an exercise to the interested reader, I'm assuming that you have a parser per file and I worry that 'stack_matched' is still a bad name for the function, but I can't think of a better one at present. With these changes in place, your while loop becomes:

$html = $parser->do_global_replace->html;
[download]

I still worry mind. Now I'm worried that the parser is doing too much...

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