The current implementation of the FindBugs plugin and FindBugs task supply a list of source files to the FindBugs process. The information is supplied by the command line switch “-sourcepath”.
In the generated XML output file each source file is registered in a … element hinting at the actual usage of the switch. Those SrcDir-Elements than cause problems with tools relying on this information. See: https://github.com/jenkinsci/findbugs-plugin/pull/5
It seems impossible to make the FindBugs task use source directories instead of files because it extends SourceTask.