Hi, this is Scott Burson at HP Fortify. As you probably recall, we bundle FindBugs with our SCA security-oriented static analyzer product. It was originally our intention to keep up with FindBugs releases, but we stopped doing that before I joined. Anyway, I have now upgraded our bundled FindBugs from 1.3.7 to 3.0.1. In the process I hit a small bug: the feature that allows us to pass command line arguments by putting them in a file, and putting the name of the file on the command line prefixed with an "@", stopped working somewhere between these two versions. (I suspect you added this feature at our request to begin with; I think it's to work around command line length limitations on Windows.)
You can find a patch at https://code.google.com/r/gyro-findbugs/ .
This link will take you directly to the patch: https://code.google.com/r/gyro-findbugs/source/detail?r=ddfb4c1f36fedd4dfb72d88458de10ae3fb887dc
Fixed. Thanks.