I was excited to stumble upon autolink references feature you just added. Unfortunately, it seems to be to JIRA specific. Pivotal tracker looks for commit messages like this:
Blah blah blah blah [#12345]
where 12345 is the issue number. Would be nice if you could support that, all you need to do is to relax your prefix requirements to allow things like spaces and non alpha characters. Using ’ [#’ as a prefix would do the trick.