Go to the reconsideration request page. Click Check Disavowed Links. Click Disavow links. Click Choose file. Select the file you want to upload, and click Submit.
OK, I take it back. Google didn't swipe the idea from Bing-- their Disavow is simply part of the ordinary wmt suite. This one's on a completely different level. Just finding the Reconsideration Request Page was an expedition of its own. (Never been there before. I'm not big enough to get stomped. That nearby 950-penalty thread makes me grateful I show up in searches at all.)
But I still wish their computer had the brains to see that calls to piwik.php aren't links. It makes it look as if I'm gratuitously linking to myself, which can't possibly be healthy :(