Project issue link filter doesn't handle <pre> or <code> with newlines

Since #493074: Back-link to the commit as a comment on the related issue. went live, I've noticed some weird inconsistencies with how the project issue link filter (e.g. #304808: Usability: Add project issue URL filter) works. For example:

https://drupal.org/node/1365536#comment-8808067

Sometimes the [#x] part is being ignored (as it should, since all this is wrapped in <pre>) and sometimes it's being expanded.

Upon closer inspection, the difference is if there's a newline inside the <pre> or <code> tag. If there's no newline, we properly ignore this case. If there's a newline, we don't recognize it as escaped text and the filter fires. Behold:

No newline:

[#304808]

With newline:

[#304808]
Stuff on a newline

The regexp in question is this:

   $regex = '(?:(?<!\w)\[#\d+(?:-[\d\.]+)?(@)?\](?!\w))|<pre>.*?<\/pre>|<code>.*?<\/code>|<a(?:[^>"\']|"[^"]*"|\'[^\']*\')*>.*?<\/a>';

The interesting parts are the | clauses for <pre>, <code> and <a>. We're just doing .*? in there, which by default does *not* match newlines. So, I think we just want the 's' modifier on the regexp (PCRE_DOTALL) so that '.' consumes anything, including a newline.