Using "excludes" config in Findbugs and Checkstyle plugin in Gradle

SourceTask#exclude filters source files. However, FindBugs primarily operates on class files, which you'll have to filter as well. Try something like:

tasks.withType(FindBugs) {
    exclude '**/org/jsense/serialize/protobuf/gen/*'
    classes = classes.filter { 
        !it.path.contains(new File("org/jsense/serialize/protobuf/gen/").path) 
    }
}

PS: It could be that filtering source files makes no difference (and therefore isn't necessary) in case of FindBugs. (I haven't tried though.)

If someone looking for a modern day solution:
For checkstyle, you can use something like this in build.gradle:

checkstyleMain.exclude '**/org/jsense/serialize/protobuf/gen/**'

If you want to exclude more than one path
solution 1:

checkstyleMain.exclude '**/org/jsense/serialize/protobuf/gen/**'
checkstyleMain.exclude '**/org/example/some/random/path/**'

solution 2:

checkstyleMain {
    setExcludes(new HashSet(['**/org/jsense/serialize/protobuf/gen/**', '**/org/example/some/random/path/**']))
}