Trying to fix line-endings with git filter-branch, but having no luck

I have been bitten by the windows/linux line-ending issue with git. It seems, via github, msysgit, and other sources, that the best solution is to have your local repos set to use linux-style line endings, but set core.autocrlf to true. Unfortunately, I didn't do this early enough, so now every time I pull changes the line endings are borked.